Oligonucleotide-based probes for detection of bacterial nucleases

ABSTRACT

The present invention relates to a rapid detection of microbial-associated nuclease activity with chemically modified nuclease (e.g., ribonuclease) substrates, and probes and compositions useful in detection assays. Accordingly, in certain embodiments, the present invention provides a probe for detecting a microbial endonuclease comprising a substrate oligonucleotide of 2-30 nucleotides in length, a fluorescence-reporter group operably linked to the oligonucleotide, and a fluorescence-quencher group operably linked to the oligonucleotide. The fluorescence-reporter group and the fluorescence-quencher group are separated by at least one RNAse-cleavable residue, e.g., RNA base.

RELATED APPLICATION

This application claims priority under 35 U.S.C. 119(e) to provisionalapplication U.S. Ser. No. 61/530,246 filed Sep. 1, 2011 and toprovisional application U.S. Ser. No. 61/593,595 filed Feb. 1, 2012,which applications are incorporated hereby by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under AI083211 awardedby the National Institutes of Health. The government has certain rightsin the invention.

BACKGROUND OF THE INVENTION

Chemical moieties that quench fluorescent light operate through avariety of mechanisms, including fluorescence resonance energy transfer(FRET) processes and ground state quenching. FRET is one of the mostcommon mechanisms of fluorescent quenching and can occur when theemission spectrum of the fluorescent donor overlaps the absorbancespectrum of the quencher and when the donor and quencher are within asufficient distance known as the Forster distance. The energy absorbedby a quencher can subsequently be released through a variety ofmechanisms depending upon the chemical nature of the quencher. Capturedenergy can be released through fluorescence or through nonfluorescentmechanisms, including charge transfer and collisional mechanisms, or acombination of such mechanisms. When a quencher releases captured energythrough nonfluorescent mechanisms FRET is simply observed as a reductionin the fluorescent emission of the fluorescent donor.

Although FRET is the most common mechanism for quenching, anycombination of molecular orientation and spectral coincidence thatresults in quenching is a useful mechanism for quenching by thecompounds of the present invention. For example, ground-state quenchingcan occur in the absence of spectral overlap if the fluorophore andquencher are sufficiently close together to form a ground state complex.

Quenching processes that rely on the interaction of two dyes as theirspatial relationship changes can be used conveniently to detect and/oridentify nucleotide sequences and other biological phenomena. As notedpreviously, the energy transfer process requires overlap between theemission spectrum of the fluorescent donor and the absorbance spectrumof the quencher. This complicates the design of probes because not allpotential quencher/donor pairs can be used. For example, the quencherBHQ-1, which maximally absorbs light in the wavelength range of about500-550 nm, can quench the fluorescent light emitted from thefluorophore fluorescein, which has a wavelength of about 520 nm. Incontrast, the quencher BHQ-3, which maximally absorbs light in thewavelength range of about 650-700 nm would be less effective atquenching the fluorescence of fluorescein but would be quite effectiveat quenching the fluorescence of the fluorophore Cy5 which fluoresces atabout 670 nm. The use of varied quenchers complicates assay developmentbecause the purification of a given probe can vary greatly depending onthe nature of the quencher attached.

Many quenchers emit energy through fluorescence reducing the signal tonoise ratio of the probes that contain them and the sensitivity ofassays that utilize them. Such quenchers interfere with the use offluorophores that fluoresce at similar wavelength ranges. This limitsthe number of fluorophores that can be used with such quenchers therebylimiting their usefulness for multiplexed assays which rely on the useof distinct fluorophores in distinct probes that all contain a singlequencher.

Endonucleases are enzymes that cleave the phosphodiester bond within apolynucleotide (DNA or RNA) chain, in contrast to exonucleases, whichcleave phosphodiester bonds at the end of a polynucleotide chain.Typically, a restriction site, i.e., a recognition site for anendonuclease, is a palindromic sequence four to six nucleotides long(e.g., TGGATCCA).

Endonucleases, found in bacteria and archaea, are thought to haveevolved to provide a defense mechanism against invading viruses. Insidea bacterial host, the restriction enzymes selectively cut up foreign DNAin a process called restriction; host DNA is methylated by amodification enzyme (a methylase) to protect it from the restrictionenzyme's activity. Collectively, these two processes form therestriction modification system. To cut the DNA, a restriction enzymemakes two incisions, once through each sugar-phosphate backbone (i.e.each strand) of the DNA double helix.

Some cells secrete copious quantities of non-specific RNases such as Aand T1. RNases are extremely common, resulting in very short lifespansfor any RNA that is not in a protected environment. Similar torestriction enzymes, which cleave highly specific sequences ofdouble-stranded DNA, a variety of endoribonucleases that recognize andcleave specific sequences of single-stranded RNA have been recentlyclassified.

Present technologies for detection of bacterial pathogens aretime-consuming and expensive because they usually require the isolationand culturing of the bacteria. Also, many of the existing technologiesare toxic and/or use radioactive tracers. Further, technologies forimaging bacterial colonization in humans lack sensitivity. Accordingly,a rapid, inexpensive, non-toxic bacterial-specific assay is needed.

SUMMARY OF THE INVENTION

Accordingly, in certain embodiments, the present invention provides aprobe for detecting a microbial endonuclease comprising a substrateoligonucleotide of 2-30 nucleotides in length, a fluorescence-reportergroup operably linked to the oligonucleotide, and afluorescence-quencher group operably linked to the oligonucleotide. Thefluorescence-reporter group and the fluorescence-quencher group areseparated by at least one RNAse-cleavable residue, e.g., RNA base. Incertain embodiments, the fluorescence-reporter group and thefluorescence-quencher group are separated by at least oneDNAse-cleavable residue, e.g., DNA base. Such residues serve as acleavage domain for nucleases, such as ribonucleases. In certainembodiments, the oligonucleotide is 10-15 nucleotides in length. Incertain embodiments, the oligonucleotide is 11-13 nucleotides in length.In certain embodiments, the oligonucleotide comprises 0-50% purines orany value in between. In certain embodiments the oligonucleotidecomprises 100% pyrimidines. In certain embodiments one or more of thepyrimidines are chemically modified. In certain embodiments, one or moreof the pyrimidines are 2′-O-methyl modified. In certain embodiments, oneor more of the pyrimidines are 2′-fluoro modified. In certainembodiments, one or more of the purines are chemically modified. Incertain embodiments, one or more of the purines are 2′-O-methylmodified. In certain embodiments, one or more of the purines are2′-fluoro modified. In certain embodiments, the oligonucleotide is RNA.

In certain embodiments, the fluorophore is selected from the groupconsisting of the fluorophores listed in Table 1, such as for example, afluorophore that has an emission in the near infra-red range. In certainembodiments, the quencher is selected from the group consisting of thequenchers listed in Table 2. In certain embodiments, the oligonucleotideis single-stranded.

In certain embodiments, the oligonucleotide comprises both RNA and DNA.In certain embodiments, the oligonucleotide comprises a DNAdi-nucleotide, such as AA, TT or AT.

In certain embodiments, the present invention provides anoligonucleotide substrate comprising a fluorophore operably linked to afirst strand of 4-5 modified RNA nucleotides, which is operably linkedto a DNA di-nucleotide, which is operably linked to a second strand of4-6 modified RNA nucleotides, which is operably linked to at least onefluorescence quencher. In certain embodiments, the modified RNAnucleotides are 2′-O-methyl modified RNA or 2′-fluoro modified RNA. Incertain embodiments, the fluorophore is a FAM fluorophore. In certainembodiments, at least one fluorescence quencher is ZEN fluorescencequencher and/or Iowa Black fluorescence quencher. In certainembodiments, the DNA di-nucleotide consists of AA, TT or AT.

In certain embodiments, the present invention provides anoligonucleotide substrate consisting of/56-FAM/mCmUmCmGTTmCmGmUmUmC/ZEN//3IAbRQSp/ (SEQ ID NO: 5).

The present invention in certain embodiments further provides a methodof detecting a microbial infection of a sample comprising measuringfluorescence of a sample that has been contacted with a probe describedabove, wherein a fluorescence level that is greater than thefluorescence level of an uninfected control indicates that the samplehas a microbial infection. In certain embodiments, the level is at least1-100% greater than the control level. In certain embodiments, themethod is an in vitro assay. In certain embodiments, the fluorophore isFAM, TET, HEX, JOE, MAX, Cy3, or TAMRA and the quencher is IBFQ, BHQ1 orBHQ2. In certain embodiments, the fluorophore is ROX, Texas Red, Cy5, orCy5.5 and the quencher is IBRQ or BHQ2.

The present invention in certain embodiments further provides a methodof in vivo detection of a microbial infection in a mammal comprisingmeasuring fluorescence in the mammal, wherein the mammal has beenadministered a probe as described above, wherein a fluorescence levelthat is greater than the fluorescence level of an uninfected controlindicates that the sample has a microbial infection. In certainembodiments, the level is at least 1-100% greater than the controllevel. In certain embodiments, the fluorophore absorbs in the range of650-900 nm. In certain embodiments, the fluorophore is Cy5, Cy5.5, Cy7,Licor IRD700, Licor IRDye 800 CW, or Alexa 647, 660, 680, 750, 790. Incertain embodiments, the fluorophore is detectable at a depth of 7-14 cmin the mammal. In certain embodiments, the microbial infection is amycoplasma infection. In certain embodiments, the microbial infection isa Staphylococcus aureus or Streptococcus pneumoniae infection.

In certain embodiments, the present invention provides in vitro assaysfor evaluating the activity of microbial nucleases on various nucleicacid substrates. In certain embodiments the assay evaluates the activityof mycoplasma nucleases. In certain embodiments the assay evaluates theactivity of Staphylococcus aureus or Streptococcus pneumoniae nucleases.

In certain embodiments, the methods include detection of bacterialcontamination in research laboratories, medical diagnostic applicationsand medical diagnostic imaging.

In certain embodiments, the present invention provides a method fordetecting nuclease (e.g., ribonuclease or deoxyribonuclease) activity ina test sample, comprising:

-   -   (a) contacting the test sample with a substrate, thereby        creating a test reaction mixture, wherein the substrate        comprises a nucleic acid molecule comprising:        -   i. a cleavage domain comprising a single-stranded region of            RNA, the single-stranded region comprising a 2′-fluoro            modified pyrimidine or 2′-O-methyl modified pyrimidine that            renders the oligonucleotide resistant to degradation by            mammalian nucleases;        -   ii. a fluorescence reporter group on one side of the            internucleotide linkages; and        -   iii. a non-fluorescent fluorescence-quenching group on the            other side of the internucleotide linkages;    -   (b) incubating the test reaction mixture for a time sufficient        for cleavage of the substrate by a nuclease (e.g., ribonuclease        or deoxyribonuclease) in the sample; and    -   (c) determining whether a detectable fluorescence signal is        emitted from the test reaction mixture, wherein emission of a        fluorescence signal from the reaction mixture indicates that the        sample contains nuclease (e.g., ribonuclease or        deoxyribonuclease) activity.

In certain embodiments, the present invention provides a method fordetecting nuclease (e.g., ribonuclease or deoxyribonuclease) activity ina test sample, comprising:

-   -   (a) contacting the test sample with a substrate, thereby        creating a test reaction mixture, wherein the substrate        comprises a nucleic acid molecule comprising:        -   i. a cleavage domain comprising a single-stranded region,            the single-stranded region of nucleic acid comprising a            2′-fluoro modified pyrimidine or 2′-O-methyl modified            pyrimidine that renders the oligonucleotide resistant to            degradation by mammalian nucleases;        -   ii. a fluorescence reporter group on one side of the            internucleotide linkages; and        -   iii. a non-fluorescent fluorescence-quenching group on the            other side of the internucleotide linkages;    -   (b) incubating the test reaction mixture for a time sufficient        for cleavage of the substrate by a nuclease activity in the test        sample;    -   (c) determining whether a detectable fluorescence signal is        emitted from the test reaction mixture;    -   (d) contacting a control sample with the substrate, the control        sample comprising a predetermined amount of nuclease, thereby        creating a control reaction mixture;    -   (e) incubating the control reaction mixture for a time        sufficient for cleavage of the substrate by a nuclease in the        control sample; and    -   (f) determining whether a detectable fluorescence signal is        emitted from the control reaction mixture; wherein detection of        a greater fluorescence signal in the test reaction mixture than        in the control reaction mixture indicates that the test sample        contains greater nuclease activity than in the control sample,        and wherein detection of a lesser fluorescence signal in the        test reaction mixture than in the control reaction mixture        indicates that the test sample contains less nuclease activity        than in the control sample. In certain embodiments, the nucleic        acid is RNA.

As used herein, the term “nucleic acid” and “polynucleotide” refers todeoxyribonucleotides or ribonucleotides and polymers thereof in eithersingle- or double-stranded form, composed of monomers (nucleotides)containing a sugar, phosphate and a base that is either a purine orpyrimidine. Unless specifically limited, the term encompasses nucleicacids containing known analogs of natural nucleotides which have similarbinding properties as the reference nucleic acid and are metabolized ina manner similar to naturally occurring nucleotides

“Operably-linked” refers to the association two chemical moieties sothat the function of one is affected by the other, e.g., an arrangementof elements wherein the components so described are configured so as toperform their usual function.

BRIEF DESCRIPTION OF DRAWINGS

FIGS. 1A-1C. Rapid detection of mycoplasma-associated nuclease activitywith chemically modified RNAse substrates. The basis for nucleasedetection with RNAse substrates is illustrated in panel A. RNAoligonucleotides (5′-UCUCGUACGUUC-3′ purines in gray and pyrimidines inblue) with chemically modified nucleotides, labeled on the 5′-ends withFAM are not fluorescent due to the close proximity of a 3′-quencher tothe FAM. Upon degradation of the oligo, the quencher diffuses away fromthe FAM and the FAM exhibits green fluorescence. Mycoplasma-associatednuclease activity is detected with various RNAse substrates (panel B).RNAse substrates with the chemically modified RNA compositions indicatedwere co-incubated with culture media conditioned by mycoplasma-free ormycoplasma contaminated HEK cells for 4 hours at 37° C. Fluorescence ofthese reactions was then measured with a fluorescence plate reader.Background fluorescence levels determined by the fluorescence level ofeach RNAse substrate incubated in serum-free unconditioned media havebeen subtracted from each experimental value. In panel C, the RNAsesubstrate with 2′-O-methyl-modified pyrimidines was incubated with theculture supernatant or a lysate prepared from material centrifuged fromthe supernatants of mycoplasma-free or mycoplasma-contaminated HEKcells. This assay was carried out as described for B, above, except thatthe incubation was for only 1 hour.

FIG. 2. 2′-Fluoro pyrimidine and 2′-O-methyl pyrimidine substrates withTriton X-100 lysate of M. fermentans bacteria.

FIG. 3. Degradation activity of Micrococcal Nuclease and EndA Nuclease.Unmodified (RNA and DNA) and modified (2′-Fluoro pyrimidines and2′-O-Methyl pyrimidines) nucleic acid substrates were used to assay thenuclease activity profile of Micrococcal Nuclease (MN) and EndA (H160G)Nuclease. The probes consist of a 12 nucleotide long oligonucleotide,5′-UCUCGUACGUUC-3′, with the chemical modifications indicated in thefigure, flanked by a FAM (5′-modification) and a pair of fluorescencequenchers, “ZEN” and “Iowa Black” (3′-modifications). This approachallows the evaluation of nuclease activity which is indicated byincreases in fluorescence upon substrate digestion. 50 pmoles ofsubstrate were incubated with MN (1 U/μL) and EndA H160G Nuclease (2 μM)in 10 μl total volume. Imadazole was included in the EndA H160Greactions to recapitulate the enzymatic properties of the wildtypeenzyme. This mutant version of the enzyme was used because the wt enzymewas toxic to e. coli and could not be produced recombinantly in largeamounts. 50 pmoles of each substrate and buffer were used as controls.All reactions were incubated for 30 minutes at 37° C. After incubation,290 μl of buffer supplemented with 10 mM EDTA and 10 mM EGTA were addedto each sample and 95 μl of each sample were loaded in triplicate into a96-well plate (96F non-treated black microwell plate (NUNC)).Fluorescence intensity was measured with a fluorescence microplatereader (Analyst HT; Biosystems).

FIGS. 4A-4D. Digestion of various nucleic acids by bacterial nucleases.Incubation of a 12 nucleotide-long RNA oligo (UCUCGUACGUUC with a 5′-Famand a 3′-Quencher) with the indicated modifications with buffer only,RNAse A (Panel A), MN (1 unit/μl) (Panels A and B) and EndA (20 μM)(Panel B) for 1 hour at 37° C. Panel C shows digestion of a quenchedfluorescent DNA oligo with S. aureus culture supernatants (+ or −MN)incubated for 10 minutes at 37° C. Digestion results in florescenceincreases in each of the experiments in Panels A-C. Panel D shows thePAGE analysis of a 51 nucleotide-long FAM-labeled (3′-end” RNA oligowith the indicated modifications after 1 hour, 37° C. incubation withcomplete, serum-containing cell culture media or with the same mediaconditioned by HEK cells contaminated with Mycoplasma fermentans. Arrowindicates full-length RNA. Modified RNAs were not digested in mediaconditioned with uncontaminated HEK cells.

FIG. 5. Digestion of oligonucleotide substrates with variousconcentrations of micrococcal nuclease (MN).

FIG. 6. Oligonucleotide substrate plate-reader assays.

FIG. 7. Cultures of the indicated bacteria were grown to stationaryphase. Bacteria were pelleted via centrifugation and nuclease activityof supernatants was measured as described for FIG. 13. To determinebackground levels of probe fluorescence/activation in each of thebacteria-free culture broth preparations used, probes were combined witheach of the indicated broths in addition to PBS and incubated inparallel with the culture supernatant reactions. Incubation time was 15minutes.

FIG. 8A-8B. Activation of various nucleic acid probes (see Table 4 forprobe details) by MN, mouse and human serum (A), and S. aureusMN-expressing and MN-negative (Newman and UAMS-1 strains) culturesupernatants (B). 50 picomoles of each of the indicated probes wasincubated with 1 U/μl (positive control) or 0.1 U/μl MN in DPBS(includes physiological levels of calcium and magnesium), or with 90%mouse or human serum (A) or with 90% of culture supernatants of theindicated S. aureus strains (prepared as described in Materials andMethods) for 60 minutes at 37° C. After the incubations, each reactionwas divided into 3 volumes which were read in a fluorescenceplate-reader. Mean fluorescence values of all reactions with a givenprobe were normalized to the mean fluorescence measured with digestionof the probe with 1 U/μl MN. Error bars represent standard deviations ofthe plate-reader values. Background fluorescence subtractions werecarried out (prior to normalization) as follows: The fluorescence ofeach of the probes incubated in DPBS was subtracted from thecorresponding MN-containing reactions. The fluorescence of each of theprobes incubated in DPBS plus the autofluorescence of each serum (mouseor human) was subtracted from the serum-containing reactions. Thefluorescence of each of the probes incubated in unconditioned TSB wassubtracted from the corresponding S. aureus culture supernatantreactions.

FIG. 9A-9F. Activation of the Cy5.5-TT probe by MN in vitro and in micewith MN-expressing S. aureus pyomyositis. For in vitro evaluation of theCy5.5-TT nuclease-activated probe, serial dilutions of the probe werecombined with DPBS or DPBS+1 U/μl MN in 100 μl volumes and incubated at37° C. for 1 hour. Cy5.5 fluorescence was measured for each reaction ina 96-well plate in a Xenogen IVIS 200 imaging system. Controls includeDPBS (left column) and the unquenched TT probe (second column) dilutedin DPBS. To evaluate probe activation in mice with S. aureus-derivedpyomyositis, uninfected mice (n=3 mice) (A), mice with lux+MN-expressingS. aureus (Newman strain) pyomyositis (n=4 mice) (C), and mice withlux+MN-negative S. aureus (Newman strain) pyomyositis (n=4 mice) (D) inthe right thighs were imaged with Cy5.5-channel fluorescence (IVISimaging system) prior to (Bkgd) and after tail vein administration of 3nanomoles of Cy5.5-TT probe. Uninfected mice that received 3 nanomolesof unquenched TT probe (n=3 mice) (B) were imaged in the same manner,but with a shorter exposure time to avoid signal saturation.Luminescence images acquired prior to probe injections (see panels onleft) indicate the location of the infections in C and D. Note probeactivation adjacent to the infection site in C, and minimal probeactivation adjacent to infection site in D. See lookup table signaldisplay ranges (at right of luminescence and right-most fluorescenceimages) for the relationship between pseudocolors and signal strength.Fluorescence display levels are adjusted to show light levels that areabove tissue autofluorescence, fluorescence produced by the unactivatedTT probe or by bleed-through of the luminescence signal into the Cy5.5channel. Time-points listed above fluorescence images indicate the timeelapsed between probe administration and image acquisition. For imagingof probes in mice after sacrifice and dissection, mice with thigh-musclelux+, MN-expressing S. aureus pyomyositis, injected with 3 nanomolesunquenched TT probe (n=4 mice) (E) or TT probe (n=4 mice) (F) weresacrificed 45 minutes after probe injection; organs and skin wereremoved and muscle tissue was imaged with luminescence and the Cy5.5fluorescence channel. Note the lack of overlap between the probefluorescence and bacteria-derived luminescence in E, indicating that theprobe cannot access the infection site. The activated TT probefluorescence is found adjacent to, but not co-localized with, thebacteria-derived luminescence (F). Lookup table signal display ranges ofthe pseudocolored luminescence and fluorescence image data are shown atright.

FIG. 10A-10B. Activation of various nucleic acid probes (see Table 4 forprobe details) by culture supernatants (A) or cell suspensions (B) ofvarious pathogenic bacterial species. 50 picomoles of each of theindicated probes was incubated with 1 U/μl MN (positive control) in DPBSor with 90% of culture supernatants or concentrated and washed cellsuspensions of the indicated bacterial species (prepared as described inExample 6, Materials and Methods) for 60 minutes at 37° C. After theincubations, each reaction was divided into 3 volumes which were read ina fluorescence plate-reader. Mean fluorescence values of all reactionswith a given probe were normalized to the mean fluorescence measuredwith digestion of the probe with 1 U/μl MN. Error bars representstandard deviations of the plate-reader values. Background fluorescencesubtractions were carried out (prior to normalization) as follows: Thefluorescence of each of the probes incubated in DPBS was subtracted fromthe corresponding MN-containing reactions. The fluorescence of each ofthe probes incubated in the appropriate unconditioned culture broth wassubtracted from the corresponding culture supernatant reactions. Thefluorescence of each of the probes incubated in DPBS plus theautofluorescence of each appropriate bacterial suspension was subtractedfrom each bacterial suspension reaction.

DETAILED DESCRIPTION OF THE INVENTION

In certain embodiments, the present invention provides shortoligonucleotide probes (Substrates) composed of chemically modified RNAflanked with a fluorophore on one end and a fluorescence quencher on theother end. Upon cleavage of the probes by nucleases (e.g.,ribonuclease), the fluorophore diffuses away from the quencher andexhibits fluorescence. These probes are not cleaved by mammaliannucleases, but are cleaved by nucleases produced by various bacteria,including pathogenic bacteria such as Staphylococcus aureus,Streptococcus pneumoniae or Mycoplasma. The probes can thus be used todetect the presence of bacteria in biological samples such as bloodserum, cell cultures, and food, and in vivo.

The present invention relates to methods for detecting nuclease (e.g.,ribonuclease) activity in a sample, comprising: 1) incubating asynthetic Substrate or mixture of Substrates in the sample, for a timesufficient for cleavage of the Substrates(s) by a nuclease enzyme,wherein the Substrate(s) comprises a single-stranded nucleic acidmolecule containing at least one ribonucleotide or deoxyribonucleotideresidue at an internal position that functions as a nuclease (e.g.,ribonuclease) cleavage site (and in certain embodiments a 2′-fluoromodified pyrimidine or 2′-O-methyl modified pyrimidine that renders theoligonucleotide resistant to degradation by mammalian nucleases), afluorescence reporter group on one side of the cleavage sites, and afluorescence-quenching group on the other side of the cleavage site, and2) visual detection of a fluorescence signal, wherein detection of afluorescence signal indicates that a nuclease (e.g., ribonuclease)cleavage event has occurred, and, therefore, the sample containsnuclease (e.g., ribonuclease) activity. The compositions of theinvention are also compatible with other detection modalities (e.g.,fluorometry).

The Substrate oligonucleotide of the invention comprises a fluorescentreporter group and a quencher group in such physical proximity that thefluorescence signal from the reporter group is suppressed by thequencher group. Cleavage of the Substrate with a nuclease (e.g.,ribonuclease) enzyme leads to strand cleavage and physical separation ofthe reporter group from the quencher group. Separation of reporter andquencher eliminates quenching, resulting in an increase in fluorescenceemission from the reporter group. When the quencher is a so-called “darkquencher”, the resulting fluorescence signal can be detected by directvisual inspection (provided the emitted light includes visiblewavelengths). Cleavage of the Substrate compositions described in thepresent invention can also be detected by fluorometry.

In one embodiment, the synthetic Substrate is an oligonucleotidecomprising ribonucleotide residues. The synthetic Substrate can also bea chimeric oligonucleotide comprising RNase-cleavable, e.g., RNA,residues, or modified RNase-resistant RNA residues. Substratecomposition is such that cleavage is a ribonuclease-specific event andthat cleavage by enzymes that are strictly deoxyribonucleases does notoccur.

In one embodiment, the synthetic Substrate is a chimeric oligonucleotidecomprising ribonucleotide residue(s) and modified ribonucleotideresidue(s). In one embodiment, the synthetic Substrate is a chimericoligonucleotide comprising ribonucleotide residues and 2′-O-methylribonucleotide residues. In one embodiment, the synthetic Substrate is achimeric oligonucleotide comprising 2′-O-methyl ribonucleotide residuesand one or more of each of the four ribonucleotide residues, adenosine,cytosine, guanosine, and uridine. Inclusion of the four distinctribonucleotide bases in a single Substrate allows for detection of anincreased spectrum of ribonuclease enzyme activities by a singleSubstrate oligonucleotide.

In one embodiment, the synthetic Substrate is an oligonucleotidecomprising deoxyribonucleotide residues. The synthetic Substrate canalso be a chimeric oligonucleotide comprising DNase-cleavable, e.g.,DNA, residues, or modified RNase-resistant RNA residues. Substratecomposition is such that cleavage is a deoxyribonuclease-specific eventand that cleavage by enzymes that are strictly ribonucleases does notoccur.

In one embodiment, the synthetic Substrate is a chimeric oligonucleotidecomprising deoxyribonucleotide residue(s) and modified ribonucleotideresidue(s). In one embodiment, the synthetic Substrate is a chimericoligonucleotide comprising deoxyribonucleotide residues and 2′-O-methylribonucleotide residues. In one embodiment, the synthetic Substrate is achimeric oligonucleotide comprising 2′-O-methyl ribonucleotide residuesand one or more of each of the four deoxyribonucleotide residues,deoxyadenosine, deoxycytosine, deoxyguanosine, and deoxythymidine.Inclusion of the four distinct deoxyribonucleotide bases in a singleSubstrate allows for detection of an increased spectrum ofdeoxyribonuclease enzyme activities by a single Substrateoligonucleotide.

To enable visual detection methods, the quenching group is itself notcapable of fluorescence emission, being a “dark quencher”. Use of a“dark quencher” eliminates the background fluorescence of the intactSubstrate that would otherwise occur as a result of energy transfer fromthe reporter fluorophore. In one embodiment, the fluorescence quenchercomprises dabcyl (4-(4′-dimethylaminophenylazo)benzoic acid). In oneembodiment, the fluorescence quencher is comprised of QSY™7 carboxylicacid, succinimidyl ester(N,N′-dimethyl-N,N′-diphenyl-4-((5-t-butoxycarbonylaminopentyl)aminocarbonyl)piperidinylsulfonerhodamine; a diarylrhodamine derivative from MolecularProbes, Eugene, Oreg.). Any suitable fluorophore may be used as reporterprovided its spectral properties are favorable for use with the chosenquencher. A variety of fluorophores can be used as reporters, includingbut not limited to, fluorescein, tetrachlorofluorescein,hexachlorofluorescein, rhodamine, tetramethylrhodamine, Cy-dyes, TexasRed, Bodipy dyes, and Alexa dyes.

The method of the invention proceeds in two steps. First, the testsample is mixed with the Substrate reagent and incubated. Substrate canbe mixed alone with the test sample or will be mixed with an appropriatebuffer, e.g., one of a composition as described herein. Second, visualdetection of fluorescence is performed. As fluorescence above backgroundindicates fluorescence emission of the reaction product, i.e. thecleaved Substrate, detection of such fluorescence indicates that RNaseactivity is present in the test sample. The method provides that thisstep can be done with unassisted visual inspection. In particular,visual detection can be performed using a standard ultraviolet (UV)light source of the kind found in most molecular biology laboratories toprovide fluorescence excitation. Substrates of the invention can also beutilized in assay formats in which detection of Substrate cleavage isdone using a multi-well fluorescence plate reader or a tube fluorometer.

The present invention further features kits for detecting nuclease(e.g., ribonuclease) activity comprising a Substrate nucleic acid(s) andinstructions for use. Such kits may optionally contain one or more of: apositive control nuclease (e.g., ribonuclease), RNase-free water, and abuffer. It is also provided that the kits may include RNase-freelaboratory plasticware, for example, thin-walled, UV transparentmicrotubes for use with the visual detection method and/or multiwellplates for use with plate-fluorometer detection methods in ahigh-throughput format.

Accordingly, the present invention provides a method for detectingnuclease (e.g., ribonuclease) activity in a test sample, comprising: (a)contacting the test sample with a substrate, thereby creating a testreaction mixture, wherein the substrate comprises a nucleic acidmolecule comprising (i) a cleavage domain comprising a single-strandedregion, the single-stranded region comprising at least oneinternucleotide linkage (and in certain embodiments a 2′-fluoro modifiedpyrimidine or 2′-O-methyl modified pyrimidine that renders theoligonucleotide resistant to degradation by mammalian nucleases); (ii) afluorescence reporter group on one side of the internucleotide linkage;and (iii) a non-fluorescent fluorescence-quenching group on the otherside of the internucleotide linkage; (b) incubating the test reactionmixture for a time sufficient for cleavage of the substrate by aribonuclease in the sample; and (c) determining whether a detectablefluorescence signal is emitted from the test reaction mixture, whereinemission of a fluorescence signal from the reaction mixture indicatesthat the sample contains ribonuclease activity.

While the methods of the invention can be practiced without the use of acontrol sample, in certain embodiments of the invention it is desirableto assay in parallel with the test sample a control sample comprising aknown amount of RNase activity. Where the control sample is used as anegative control, the control sample, in some embodiments, contains nodetectable RNase activity. Thus, the present invention further providesa method for detecting ribonuclease activity in a test sample,comprising: (a) contacting the test sample with a substrate, therebycreating a test reaction mixture, wherein the substrate comprises anucleic acid molecule comprising: (i) a cleavage domain comprising asingle-stranded region, the single-stranded region comprising at leastone internucleotide linkage (and in certain embodiments a 2′-fluoromodified pyrimidine or 2′-O-methyl modified pyrimidine that renders theoligonucleotide resistant to degradation by mammalian nucleases); (ii) afluorescence reporter group on one side of the internucleotide linkage;and (iii) a non-fluorescent fluorescence-quenching group on the otherside of the internucleotide linkage; (b) incubating the test reactionmixture for a time sufficient for cleavage of the substrate by anuclease (e.g., ribonuclease) activity in the test sample; (c)determining whether a detectable fluorescence signal is emitted from thetest reaction mixture; (d) contacting a control sample with thesubstrate, the control sample comprising a predetermined amount ofnuclease (e.g., ribonuclease), thereby creating a control reactionmixture; (e) incubating the control reaction mixture for a timesufficient for cleavage of the substrate by a nuclease (e.g.,ribonuclease) in the control sample; (f) determining whether adetectable fluorescence signal is emitted from the control reactionmixture; wherein detection of a greater fluorescence signal in the testreaction mixture than in the control reaction mixture indicates that thetest sample contains greater nuclease (e.g., ribonuclease) activity thanin the control sample, and wherein detection of a lesser fluorescencesignal in the test reaction mixture than in the control reaction mixtureindicates that the test sample contains less nuclease (e.g.,ribonuclease) activity than in the control sample. In one embodiment,the predetermined amount of nuclease (e.g., ribonuclease) is nonuclease, such that detection of a greater fluorescence signal in thetest reaction mixture than in the control reaction mixture indicatesthat the test sample contains nuclease (e.g., ribonuclease) activity.

The methods of the invention can further entail contacting the testsample with a buffer before or during step (a).

The present invention further provides compositions and kits forpracticing the present methods. Thus, in certain embodiments, thepresent invention provides a nucleic acid comprising: (a) a cleavagedomain comprising a single-stranded region, the single-stranded regioncomprising at least one internucleotide linkage (and in certainembodiments a 2′-fluoro modified pyrimidine or 2′-O-methyl modifiedpyrimidine that renders the oligonucleotide resistant to degradation bymammalian nucleases); (b) a fluorescence reporter group on one side ofthe internucleotide linkage; and (c) a non-fluorescentfluorescence-quenching group on the other side of the internucleotidelinkage. In other embodiments, the present invention provides a kitcomprising: (a) in one container, a substrate, the substrate comprisinga nucleic acid molecule comprising a single stranded region, thesingle-stranded region comprising: (i) a cleavage domain comprising asingle-stranded region, the single-stranded region comprising at leastone internucleotide linkage 3′ to an adenosine residue, at least oneinternucleotide linkage 3′ to a cytosine residue, at least oneinternucleotide linkage 3′ to a guanosine residue, and at least oneinternucleotide linkage 3′ to a uridine residue, and wherein thecleavage domain does not comprise a deoxyribonuclease-cleavableinternucleotide linkage; (ii) a fluorescence reporter group on one sideof the internucleotide linkages; and (iii) a non-fluorescentfluorescence-quenching group on the other side of the internucleotidelinkages.

In one embodiment of the foregoing methods and compositions, the singlestranded region of the cleavage domain comprises at least oneinternucleotide linkage 3′ to an adenosine residue, at least oneinternucleotide linkage 3′ to a cytosine residue, at least oneinternucleotide linkage 3′ to a guanosine residue, and at least oneinternucleotide linkage 3′ to a uridine residue. In one embodiment, thecleavage domain does not comprise a deoxyribonuclease-cleavableinternucleotide linkage. In yet another referred embodiment, the singlestranded region of the cleavage domain comprises at least oninternucleotide linkage 3′ to an adenosine residue, at least oneinternucleotide linkage 3′ to a cytosine residue, at least oneinternucleotide linkage 3′ to a guanosine residue, and at least oneinternucleotide linkage 3′ to a uridine residue and the cleavage domaindoes not comprise a deoxyribonuclease-cleavable internucleotide linkage.

In one embodiment of the foregoing methods and compositions, the singlestranded region of the cleavage domain comprises at least oneinternucleotide linkage 3′ to a deoxyadenosine residue, at least oneinternucleotide linkage 3′ to a deoxycytosine residue, at least oneinternucleotide linkage 3′ to a deoxyguanosine residue, and at least oneinternucleotide linkage 3′ to a deoxythymidine residue. In oneembodiment, the cleavage domain does not comprise aribonuclease-cleavable internucleotide linkage. In yet another referredembodiment, the single stranded region of the cleavage domain comprisesat least one internucleotide linkage 3′ to a deoxyadenosine residue, atleast one internucleotide linkage 3′ to a deoxycytosine residue, atleast one internucleotide linkage 3′ to a deoxyguanosine residue, and atleast one internucleotide linkage 3′ to a deoxythymidine residue and thecleavage domain does not comprise a ribonuclease-cleavableinternucleotide linkage.

With respect to the fluorescence quenching group, any compound that is adark quencher can be used in the methods and compositions of theinvention. Numerous compounds are capable of fluorescence quenching,many of which are not themselves fluorescent (i.e., are dark quenchers.)In one embodiment, the fluorescence-quenching group is anitrogen-substituted xanthene compound, a substituted4-(phenyldiazenyl)phenylamine compound, or a substituted4-(phenyldiazenyl)naphthylamine compound. In certain specific modes ofthe embodiment, the fluorescence-quenching group is4-(4′-dimethylaminophenylazo)benzoic acid),N,N′-dimethyl-N,N′-diphenyl-4-((5-t-butoxycarbonylaminopentyl)aminocarbonyl)piperidinylsulfonerhodamine (sold as QSY-7™ by Molecular Probes, Eugene,Oreg.), 4′,5′-dinitrofluorescein, pipecolic acid amide (sold as QSY-33™by Molecular Probes, Eugene, Oreg.)4-[4-nitrophenyldiazinyl]phenylamine, or4-[4-nitrophenyldiazinyl]naphthylamine (sold by Epoch Biosciences,Bothell, Wash.). In other specific modes of the embodiment, thefluorescence-quenching group is Black-Hole Quenchers™ 1, 2, or 3(Biosearch Technologies, Inc.).

In certain embodiments, the fluorescence reporter group is fluorescein,tetrachlorofluorescein, hexachlorofluorescein, rhodamine,tetramethylrhodamine, a Cy dye, Texas Red, a Bodipy dye, or an Alexadye.

With respect to the foregoing methods and compositions, the fluorescencereporter group or the fluorescence quenching group can be, but is notnecessarily, attached to the 5′-terminal nucleotide of the substrate.

The nucleic acids of the invention, including those for use assubstrates in the methods of the invention, in certain embodiments aresingle-stranded RNA molecule. In other embodiments, the nucleic acids ofthe invention are chimeric oligonucleotides comprising a nucleaseresistant modified ribonucleotide residue. Exemplary RNase resistantmodified ribonucleotide residues include 2′-O-methyl ribonucleotides,2′-methoxyethoxy ribonucleotides, 2′-O-allyl ribonucleotides,2′-O-pentyl ribonucleotides, and 2′-O-butyl ribonucleotides. In one modeof the embodiment, the modified ribonucleotide residue is at the5′-terminus or the 3′-terminus of the cleavage domain. In yet otherembodiments, the nucleic acids of the invention are chimericoligonucleotides comprising a deoxyribonuclease resistant modifieddeoxyribonucleotide residue. In specific modes of the embodiments, thedeoxyribonuclease resistant modified deoxyribonucleotide residue is aphosphotriester deoxyribonucleotide, a methylphosphonatedeoxyribonucleotide, a phosphoramidate deoxyribonucleotide, aphosphorothioate deoxyribonucleotide, a phosphorodithioatedeoxyribonucleotide, or a boranophosphate deoxyribonucleotide. In yetother embodiments of the invention, the nucleic acids of the inventioncomprise a ribonuclease-cleavable modified ribonucleotide residue.

The nucleic acids of the invention, including those for use assubstrates in the methods of the invention, are at least 3 nucleotidesin length, such as 5-30 nucleotides in length. In certain specificembodiments, the nucleic acids of the invention are 5-20, 5-15, 5-10,7-20, 7-15 or 7-10 nucleotides in length.

In certain embodiments, the fluorescence-quenching group of the nucleicacids of the invention is 5′ to the cleavage domain and the fluorescencereporter group is 3′ to the cleavage domain. In a specific embodiment,the fluorescence-quenching group is at the 5′ terminus of the substrate.In another specific embodiment, the fluorescence reporter group is atthe 3′ terminus of the substrate.

In certain embodiments, the fluorescence reporter group of the nucleicacids of the invention is 5′ to the cleavage domain and thefluorescence-quenching group is 3′ to the cleavage domain. In a specificembodiment, the fluorescence reporter group is at the 5′ terminus of thesubstrate. In another specific embodiment, the fluorescence-quenchinggroup is at the 3′ terminus of the substrate.

In one embodiment of the invention, a nucleic acid of the inventioncomprising the formula: 5′-N₁-n-N₂-3′, wherein: (a) “N₁” represents zeroto five 2′-modified ribonucleotide residues; (b) “N₂” represents one tofive 2′-modified ribonucleotide residues; and (c) “n” represents one toten, such as four to ten unmodified ribonucleotide residues. In acertain specific embodiment, “N₁” represents one to five 2′-modifiedribonucleotide residues. In certain modes of the embodiment, thefluorescence-quenching group or the fluorescent reporter group isattached to the 5′-terminal 2′-modified ribonucleotide residue of N₁.

In the nucleic acids of the invention, including nucleic acids with theformula: 5′-N₁-n-N₂-3′, the fluorescence-quenching group can be 5′ tothe cleavage domain and the fluorescence reporter group is 3′ to thecleavage domain; alternatively, the fluorescence reporter group is 5′ tothe cleavage domain and the fluorescence-quenching group is 3′ to thecleavage domain.

With respect to the kits of the invention, in addition to comprising anucleic acid of the invention, the kits can further comprise one or moreof the following: a ribonuclease; ribonuclease-free water, a buffer, andribonuclease-free laboratory plasticware.

Substrate Oligonucleotides

Compositions of the invention comprise synthetic oligonucleotideSubstrates that are substrates for nuclease (e.g., ribonuclease)enzymes. Substrate oligonucleotides of the invention comprise: 1) one ormore nuclease-cleavable bases, e.g., RNA bases, some or all of whichfunction as scissile linkages, 2) a fluorescence-reporter group and afluorescence-quencher group (in a combination and proximity that permitsvisual FRET-based fluorescence quenching detection methods), and 3) mayoptionally contain RNase-resistant modified RNA bases,nuclease-resistant DNA bases, or unmodified DNA bases. Syntheticoligonucleotide RNA-DNA chimeras wherein the internal RNA bonds functionas a scissile linkage are described in U.S. Pat. Nos. 6,773,885 and7,803,536. The fluorescence-reporter group and the fluorescence-quenchergroup are separated by at least one RNAse-cleavable residue, e.g., RNAbase. Such residues serve as a cleavage domain for ribonucleases.

In certain embodiments, the substrate oligonucleotide probes aresingle-stranded or double-stranded oligoribonucleotides. In certainembodiments, the oligonucleotide probes are composed of modifiedoligoribonucleotides. The term “modified” encompasses nucleotides with acovalently modified base and/or sugar. For example, modified nucleotidesinclude nucleotides having sugars which are covalently attached to lowmolecular weight organic groups other than a hydroxyl group at the 3′position and other than a phosphate group at the 5′ position. Thusmodified nucleotides may also include 2′ substituted sugars such as2′-O-methyl-; 2-O-alkyl; 2-O-allyl; 2′-S-alkyl; 2′-S-allyl; 2′-fluoro-;2′-halo or 2-azido-ribose, carbocyclic sugar analogues a-anomericsugars; epimeric sugars such as arabinose, xyloses or lyxoses, pyranosesugars, furanose sugars, and sedoheptulose. In certain embodiments, theSubstrate includes, but is not limited to, 2′-O-methyl RNA,2′-methoxyethoxy RNA, 2′-O-allyl RNA, 2′-O-pentyl RNA, and 2′-O-butylRNA. In certain embodiments, the substrate is an RNA-2′-O-methyl RNAoligonucleotide having the general structure 5′ r-NnN-q 3′, where ‘N’represents from about one to five 2′-modified ribonucleotide residues,‘n’ represents one to ten unmodified ribonucleotide residues, representsa fluorescence reporter group, and ‘q’ represents a fluorescencequencher group. The 5′- and 3′-position of reporter and quencher areinterchangeable. In one embodiment, the fluorescence reporter group andthe fluorescence quencher group are positioned at or near opposing endsof the molecule. It is not important which group is placed at or nearthe 5′-end versus the 3′-end. It is not required that the reporter andquencher groups be end modifications, however positioning these groupsat termini simplifies manufacture of the Substrate. The fluorescencereporter group and the fluorescence quencher group may also bepositioned internally so long as an RNA scissile linkage lies betweenreporter and quencher.

Modified nucleotides are known in the art and include, by example andnot by way of limitation, alkylated purines and/or pyrimidines; acylatedpurines and/or pyrimidines; or other heterocycles. These classes ofpyrimidines and purines are known in the art and include,pseudoisocytosine; N4, N4-ethanocytosine; 8-hydroxy-N6-methyladenine;4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil; 5-fluorouracil;5-bromouracil; 5-carboxymethylaminomethyl-2-thiouracil;5-carboxymethylaminomethyl uracil; dihydrouracil; inosine;N6-isopentyl-adenine; 1-methyladenine; 1-methylpseudouracil;1-methylguanine; 2,2-dimethylguanine; 2-methyladenine; 2-methylguanine;3-methylcytosine; 5-methylcytosine; N6-methyladenine; 7-methylguanine;5-methylaminomethyl uracil; 5-methoxy amino methyl-2-thiouracil;β-D-mannosylqueosine; 5-methoxycarbonylmethyluracil; 5-methoxyuracil;2-methylthio-N6-isopentenyladenine; uracil-5-oxyacetic acid methylester; psueouracil; 2-thiocytosine; 5-methyl-2 thiouracil, 2-thiouracil;4-thiouracil; 5-methyluracil; N-uracil-5-oxyacetic acid methylester;uracil 5-oxyacetic acid; queosine; 2-thiocytosine; 5-propyluracil;5-propylcytosine; 5-ethyluracil; 5-ethylcytosine; 5-butyluracil;5-pentyluracil; 5-pentylcytosine; and 2,6,-diaminopurine;methylpsuedouracil; 1-methylguanine; 1-methylcytosine.

The oligonucleotides of the invention are synthesized using conventionalphosphodiester linked nucleotides and synthesized using standard solidor solution phase synthesis techniques which are known in the art.Linkages between nucleotides may use alternative linking molecules. Forexample, linking groups of the formula P(O)S, (thioate); P(S)S,(dithioate); P(O)NR′2; P(O)R′; P(O)OR6; CO; or CONR′2 wherein R is H (ora salt) or alkyl (1-12C) and R6 is alkyl (1-9C) is joined to adjacentnucleotides through —O— or —S—.

In certain embodiments of the present invention, the oligonucleotideshave additional modifications, such as 2′O-methyl modification of thepyrimidines. In other embodiments, all of the nucleotides in theoligonucleotides are 2′O-methyl modified. Alternatively, thepyrimidines, or all the nucleotides, may be modified with 2′-fluoros(both pyrimidines and purines).

The oligonucleotides are short, such as between 2-30 nucleotides inlength (or any value in between). In certain embodiments, thatoligonucleotide is between 10-15 nucleotides in length. In certainembodiments, that oligonucleotide is between 11-13 nucleotides inlength. In general, shorter sequences will give better signal to noiseratios than longer probes and will therefore be more sensitive. However,in certain embodiments, shorter probes might not be the best substratefor the nuclease, so some degree of empiric optimization for length isneeded. In certain embodiments, the oligonucleotide comprises 0-50%purines (or any value in between). In certain embodiments theoligonucleotide comprises 100% pyrimidines.

It should be noted that the specific sequence of the oligonucleotide isnot critical. Certain combinations of purines and pyrimidines aresusceptible to bacterial endonucleases, while resisting mammaliannucleases. Endonucleases are enzymes that cleave the phosphodiester bondwithin a polynucleotide chain, in contrast to exonucleases, which cleavephosphodiester bonds at the end of a polynucleotide chain. Thesebacterial nucleases are not sequence-specific like restriction enzymes,which typically require a recognition site and a cleavage pattern. Someendonucleases cleave single-stranded nucleic acid molecules, whileothers cleave double-stranded nucleic acid molecules. For example, thedata below show a time-course of activity of the mycoplasma-derivednuclease and demonstrate that the mycoplasma nuclease can digest avariety of distinct sequences. The earliest time-point shows partialdegradation of the 51 nt long sequence modified with either 2′-fluoro or2′-O-methyl pyrimidines, with intermediate degradation products clearlyvisible. Each of the degradation products of intermediate size is infact a distinct substrate and these are clearly being digested as seenin the later time points.

Fluorophores

In certain embodiments, the oligonucleotides of the present inventionare operably linked to one or more fluorophores, which may also becalled a “fluorescent tag.” A fluorophore is a molecule that absorbslight (i.e. excites) at a characteristic wavelength and emits light(i.e. fluoresces) at a second lower-energy wavelength. Fluorescencereporter groups that can be incorporated into Substrate compositionsinclude, but are not limited to, fluorescein, tetrachlorofluorescein,hexachlorofluorescein, tetramethylrhodamine, rhodamine,cyanine-derivative dyes, Texas Red, Bodipy, and Alexa dyes.Characteristic absorption and emission wavelengths for each of these arewell known to those of skill in the art.

A fluorescence quencher is a molecule that absorbs or releases energyfrom an excited fluorophore (i.e., reporter), returning the fluorophoreto a lower energy state without fluorescence emission at the wavelengthcharacteristic of that fluorophore. For quenching to occur, reporter andquencher must be in physical proximity. When reporter and quencher areseparated, energy absorbed by the reporter is no longer transferred tothe quencher and is instead emitted as light at the wavelengthcharacteristic of the reporter. Appearance of a fluorescent signal fromthe reporter group following removal of quenching is a detectable eventand constitutes a “positive signal” in the assay of the presentinvention, and indicates the presence of RNase in a sample.

Fluorescence quencher groups include molecules that do not emit anyfluorescence signal (“dark quenchers”) as well as molecules that arethemselves fluorophores (“fluorescent quenchers”). Substratecompositions that employ a “fluorescent quencher” will emit light bothin the intact and cleaved states. In the intact state, energy capturedby the reporter is transferred to the quencher via FRET and is emittedas light at a wavelength characteristic for the fluorescent quencher. Inthe cleaved state, energy captured by the reporter is emitted as lightat a wavelength characteristic for the reporter. When compositions thatemploy fluorescent quenchers are used in a FRET assay, detection must bedone using a fluorometer. In certain embodiments, Substrate compositionsthat employ a “dark quencher” will emit light only in the cleaved state,enabling signal detection to be performed visually (detection may alsobe done using a fluorometer). Visual detection is rapid, convenient, anddoes not require the availability of any specialized equipment. It isdesirable for an RNase detection assay to have visual detection methodas an available option. Substrate compositions employing a “darkquencher” enable a visual detection ribonuclease assay while Substratecompositions employing a “fluorescent quencher” are incompatible with avisual detection assay.

In one embodiment of the invention, the Substrate is comprised of afluorescence quencher group that does not itself emit a fluorescencesignal, i.e. is a “dark quencher”. “Dark quenchers” useful incompositions of the invention include, but are not limited to, dabcyl,QSY™-7, QSY-33 (4′,5-dinitrofluorescein, pipecolic acid amide) andBlack-Hole Quenchers™1, 2, and 3 (Biosearch Technologies, Novato,Calif.). Assay results (i.e., signal from cleaved Substrate) can thus bedetected visually. Optionally, the fluorescence signal can be detectedusing a fluorometer or any other device capable of detecting fluorescentlight emission in a quantitative or qualitative fashion.

In certain embodiments, the fluorophore is one or more of thefluorophores listed in Table 1.

TABLE 1 Excitation Emission Probe (nm) (nm) Hydroxycoumarin 325 386Alexa fluor 325 442 Aminocoumarin 350 445 Methoxycoumarin 360 410Cascade Blue (375); 401 423 Pacific Blue 403 455 Pacific Orange 403 551Lucifer yellow 425 528 Alexa fluor 430 430 545 NBD 466 539R-Phycoerythrin (PE) 480; 565 578 PE-Cy5 conjugates 480; 565; 650 670PE-Cy7 conjugates 480; 565; 743 767 Red 613 480; 565 613 PerCP 490 675Cy2 490 510 TruRed 490, 675 695 FluorX 494 520 Fluorescein 495 519 FAM495 515 BODIPY-FL 503 512 TET 526 540 Alexa fluor 532 530 555 HEX 535555 TRITC 547 572 Cy3 550 570 TMR 555 575 Alexa fluor 546 556 573 Alexafluor 555 556 573 Tamara 565 580 X-Rhodamine 570 576 Lissamine RhodamineB 570 590 ROX 575 605 Alexa fluor 568 578 603 Cy3.5 581 581 596 TexasRed 589 615 Alexa fluor 594 590 617 Alexa fluor 633 621 639 LC red 640625 640 Allophycocyanin (APC) 650 660 Alexa fluor 633 650 688 APC-Cy7conjugates 650; 755 767 Cy5 650 670 Alexa fluor 660 663 690 Cy5.5 675694 LC red 705 680 710 Alexa fluor 680 679 702 Cy7 743 770 IRDye 800 CW774 789

In certain in vivo embodiments, the fluorophore emits in the nearinfrared range, such as in the 650-900 nm range. (Weissleder et al.,“Shedding light onto live molecular targets, Nature Medicine, 9:123-128(2003)).

Fluorescence Quencher Group

In certain embodiments, the oligonucleotides of the present inventionare operably linked to one or more fluorescence quencher group or“quencher.”

In certain embodiments, the quencher is one or more of the quencherslisted in Table 2.

TABLE 2 Absorption Maximum Quencher (nm) DDQ-I 430 Dabcyl 475 Eclipse530 Iowa Black FQ 532 BHQ-1 534 QSY-7 571 BHQ-2 580 DDQ-II 630 IowaBlack RQ 645 QSY-21 660 BHQ-3 670 IRDye QC-1 737

Additional quenchers are described in U.S. Pat. No. 7,439,341, which isincorporated by reference herein.

Linkers

In certain embodiments, the oligonucleotide is linked to the fluorophoreand/or quencher by means of a linker.

In certain embodiments, an aliphatic or ethylene glycol linker (as arewell known to those will skill in the art) is used. In certainembodiments, the linker is a phosphodiester linkage. In certainembodiments, the linker is a phosphorothioate linkage. In certainembodiments, other modified linkages between the modifier groups likedyes and quencher and the bases are used in order to make these linkagesmore stabile, thereby limiting degradation to the nucleases.

In certain embodiments, the linker is a binding pair. In certainembodiments, the “binding pair” refers to two molecules which interactwith each other through any of a variety of molecular forces including,for example, ionic, covalent, hydrophobic, van der Waals, and hydrogenbonding, so that the pair have the property of binding specifically toeach other. Specific binding means that the binding pair members exhibitbinding to each other under conditions where they do not bind to anothermolecule. Examples of binding pairs are biotin-avidin, hormone-receptor,receptor-ligand, enzyme-substrate, IgG-protein A, antigen-antibody, andthe like. In certain embodiments, a first member of the binding paircomprises avidin or streptavidin and a second member of the binding paircomprises biotin.

In certain embodiments, the oligonucleotide is linked to the fluorophoreand/or quencher by means of a covalent bond.

In certain embodiments, the oligonucleotide probe, i.e., anoligonucleotide that is operably linked to a fluorophore and quencher,is also operably linked to a solid substrate. For example, theoligonucleotide probe may be linked to a magnetic bead.

Chemistries that can be used to link the fluorophores and quencher tothe oligonucleotide are known in the art, such as disulfide linkages,amino linkages, covalent linkages, etc. In certain embodiments,aliphatic or ethylene glycol linkers that are well known to those withskill in the art can be used. In certain embodiments phosphodiester,phosphorothioate and/or other modified linkages between the modifiergroups like dyes and quencher are used. These linkages provide stabilityto the probes, thereby limiting degradation to nucleobases. Additionallinkages and modifications can be found on the world-wide-web attrilinkbiotech.com/products/oligo/oligo_modifications.asp.

Detection Compositions

In certain embodiments, the probes described above can be prepared aspharmaceutically-acceptable compositions. In certain embodiments, theprobes are administered so as to result in the detection of a microbialinfection. The amount administered will vary depending on variousfactors including, but not limited to, the composition chosen, theparticular disease, the weight, the physical condition, and the age ofthe mammal. Such factors can be readily determined by the clinicianemploying animal models or other test systems, which are well known tothe art.

Pharmaceutical formulations, dosages and routes of administration fornucleic acids are generally known in the art. The present inventionenvisions detecting a microbial infection in a mammal by theadministration of a probe of the invention. Both local and systemicadministration is contemplated.

One or more suitable unit dosage forms of the probe of the invention canbe administered by a variety of routes including parenteral, includingby intravenous and intramuscular routes, as well as by direct injectioninto the diseased tissue. The formulations may, where appropriate, beconveniently presented in discrete unit dosage forms and may be preparedby any of the methods well known to pharmacy. Such methods may includethe step of bringing into association the probe with liquid carriers,solid matrices, semi-solid carriers, finely divided solid carriers orcombinations thereof, and then, if necessary, introducing or shaping theproduct into the desired delivery system.

When the probes of the invention are prepared for administration, incertain embodiments they are combined with a pharmaceutically acceptablecarrier, diluent or excipient to form a pharmaceutical formulation, orunit dosage form. The total active ingredient (i.e., probe) in suchformulations include from 0.1 to 99.9% by weight of the formulation. A“pharmaceutically acceptable” is a carrier, diluent, excipient, and/orsalt that is compatible with the other ingredients of the formulation,and not deleterious to the recipient thereof. The active ingredient foradministration may be present as a powder or as granules, as a solution,a suspension or an emulsion.

Pharmaceutical formulations containing the probe of the invention can beprepared by procedures known in the art using well known and readilyavailable ingredients. The therapeutic agents of the invention can alsobe formulated as solutions appropriate for parenteral administration,for instance by intramuscular, subcutaneous or intravenous routes.

The pharmaceutical formulations of probe of the invention can also takethe form of an aqueous or anhydrous solution or dispersion, oralternatively the form of an emulsion or suspension.

Thus, probe may be formulated for parenteral administration (e.g., byinjection, for example, bolus injection or continuous infusion) and maybe presented in unit dose form in ampules, pre-filled syringes, smallvolume infusion containers or in multi-dose containers with an addedpreservative. The probe may take such forms as suspensions, solutions,or emulsions in oily or aqueous vehicles, and may contain formulatoryagents such as suspending, stabilizing and/or dispersing agents.Alternatively, the probe may be in powder form, obtained by asepticisolation of sterile solid or by lyophilization from solution, forconstitution with a suitable vehicle, e.g., sterile, pyrogen-free water,before use.

The pharmaceutical formulations of the present invention may include, asoptional ingredients, pharmaceutically acceptable carriers, diluents,solubilizing or emulsifying agents, and salts of the type that arewell-known in the art. Specific non-limiting examples of the carriersand/or diluents that are useful in the pharmaceutical formulations ofthe present invention include water and physiologically acceptablebuffered saline solutions such as phosphate buffered saline solutions pH7.0-8.0, saline solutions, and water.

Substrate Synthesis

Synthesis of the nucleic acid Substrate of the invention can beperformed using solid-phase phosphoramidite chemistry (U.S. Pat. No.6,773,885) with automated synthesizers, although other methods ofnucleic acid synthesis (e.g., the H-phosphonate method) may be used.Chemical synthesis of nucleic acids allows for the production of variousforms of the nucleic acids with modified linkages, chimericcompositions, and nonstandard bases or modifying groups attached inchosen places throughout the nucleic acid's entire length.

Detection Methods

In certain embodiments, the present invention provides methods fordetecting bacteria in a sample in vitro or in vivo. The method of theinvention proceeds in the following steps: combine “test sample” withSubstrate(s) to produce a mixture, the mixture being the Assay Mix,incubate, and detect fluorescence signal. “Test sample” refers to anymaterial being assayed for ribonuclease activity and in certainembodiments, will be a liquid. Solids can be indirectly tested for thepresence of RNase contamination by washing or immersion in solvent,e.g., water, followed by assay of the solvent.

For example, one can contact a sample with an oligonucleotide probe asdescribed herein, and detect the presence of bacterial endonucleasesusing a florometer. Alternatively, oligonucleotide probes orcompositions can be administered in vivo to a patient (e.g. injected insitu into a mammal) and fluorescence in the organism can be measured. Incertain embodiments, the in vivo fluorescence can be measured to a depthof about 7-14 cm. Thus, in certain embodiments, the probes of thepresent invention can be use in medical diagnostic applications andmedical diagnostic imaging.

In certain embodiments, the probes of the present invention are alsouseful to detect bacterial contamination in settings such as researchlaboratories.

Assay Mix.

The Substrate is mixed and incubated with the test sample. This mixtureconstitutes the Assay Mix. Ideally, the Assay Mix is a small volume,from about 1 μl to about 10 mls, or, from about 10 to 100 μl. Theprecise volume of the Assay Mix will vary with the nature of the testsample and the detection method. Optionally, a buffer can be added tothe Assay Mix. Nucleases, including some ribonucleases, require thepresence of divalent cations for maximum activity and providing anoptimized buffered solution can increase the reaction rate and therebyincrease assay sensitivity. Buffers of different composition can beused, as described in U.S. Pat. No. 6,773,885. In certain embodiments,control reactions are included, but are not essential. A NegativeControl Mix, for example, comprises a solution of Substrate in water orbuffer without any test sample or added nuclease. In this control, theSubstrate should remain intact (i.e., without fluorescence emission). Ifthe Negative Control Mix results in positive signal, then the quality ofall reagents is suspect and fresh reagents should be employed. Possiblecauses of a signal in a Negative Control include degradation of theSubstrate or contamination of any component reagent with ribonucleaseactivity. A Positive Control Mix, for example, comprises a solution ofSubstrate in water or buffer plus a known, active RNase enzyme. If thePositive Control Mix results in a negative signal, then the quality ofall reagents is suspect and fresh reagents should be employed. Possiblecauses of a negative Positive Control Mix include defective Substrate orcontamination of any component reagent with a ribonuclease inhibitor.Any RNase that cleaves the Substrate can be employed for use in thePositive Control Mix. In one embodiment, RNase A is used, as this enzymeis both inexpensive and readily available. Alternatively, RNase 1 can beused. RNase 1 is heat labile and is more readily decontaminated fromlaboratory surfaces.

Incubation.

The Assay Mix (e.g., the test sample plus Substrate) is incubated.Incubation time and condition can vary from a few minutes to 24 hours orlonger depending upon the sensitivity required. Incubation times of onehour or less are desirable. Ribonucleases are catalytic. Increasingincubation time should therefore increase sensitivity of the Assay,provided that background cleavage of the Substrate (hydrolysis) remainslow. As is evident, assay background is stable over time and Assaysensitivity increases with time of incubation. Incubation temperaturecan generally vary from room temperature to 37.degree. C. but may beadjusted to the temperature optimum of a specific ribonuclease suspectedas being present as a contaminant.

Signal Detection.

Fluorescence emission can be detected using a number of techniques (U.S.Pat. No. 6,773,885). In one method of detection, visual inspection isutilized. Visual detection is rapid, simple, and can be done withoutneed of any specialized equipment. Alternatively, detection can be doneusing fluorometry or any other method that allows for qualitative orquantitative assessment of fluorescent emission.

Visual Detection Method.

Following incubation, the Assay Mix is exposed to UV light to provideexcitation of the fluorescence reporter group. An Assay Mix in which theSubstrate remains intact will not emit fluorescent signal and willvisually appear clear or dark. Absence of fluorescence signalconstitutes a negative assay result. An Assay Mix in which the Substratehas been cleaved will emit fluorescent signal and will visually appearbright. Presence of fluorescence signal constitutes a positive assayresult, and indicates the presence of RNase activity in the sample. Thevisual detection method is primarily intended for use as a qualitativeribonuclease assay, with results being simply either “positive” or“negative”. However, the assay is crudely quantitative in that a brightfluorescent signal indicates higher levels of RNase contamination than aweak fluorescent signal.

The Assay Mix will ideally constitute a relatively small volume, forexample 10 to 100 μl, although greater or lesser volumes can beemployed. Small volumes allow for maintaining high concentrations ofSubstrate yet conserves use of Substrate. The visual detection Assay inone embodiment uses 50 pmoles of Substrate at a concentration of 0.5 μMin a 100 μl final volume Assay Mix. Lower concentration of Substrate(e.g., below 0.1 uM) will decrease assay sensitivity. Higherconcentrations of Substrate (e.g., above 1 μM) will increase backgroundand will unnecessarily consume Substrate.

Steps (mixing, incubating, detecting), can be performed in one tube. Inone embodiment, the tube is a small, thin-walled, UV transparentmicrofuge tube, although tubes of other configuration may be used. A“short wave” UV light source emitting at or around 254 nm is used in oneembodiment for fluorescence excitation. A “long wave” UV light sourceemitting at or around 300 nm can also be employed. A high intensity,short wave UV light source will provide for best sensitivity. UV lightsources of this kind are commonly found in most molecular biologylaboratories. Visual detection can be performed at the laboratory benchor in the field, however sensitivity will be improved if done in thedark.

Fluorometric Detection Method.

Following incubation fluorescence emission can be detected using afluorometer. Fluorometric detection equipment includes, but is notlimited to, single sample cuvette devices and multiwell plate readers.As before, mixing, incubation, and detection can be performed in thesame vessel. Use of a multiwell plate format allows for small samplevolumes, such as 200 μl or less, and high-throughput robotic processingof many samples at once. This format is used in certain industrial QCsettings. The method also provides for the Assay to be performed inRNase free cuvettes. As before, mixing, incubation, and detection can beperformed in the same vessel. Use of fluorometric detection allows forhighly sensitive and quantitative detection.

Kits

The present invention further includes kits for detecting ribonucleaseactivity in a sample, comprising Substrate nucleic acid(s) andinstructions for use. Such kits may optionally contain one or more of: apositive control ribonuclease, RNase-free water, a buffer, and otherreagents. The kits may include RNase-free laboratory plasticware, suchas thin-walled, UV transparent microtubes and/or multiwell plates foruse with the visual detection method and multiwell plates for use withplate-fluorometer detection methods.

One kit of the invention includes a universal Substrate, the Substratebeing sensitive to a broad spectrum of ribonuclease activity. The kit isintended to detect ribonuclease activity from a variety of sources. Theassay is compatible with visual detection. In certain embodiments, theSubstrate will be provided in dry form in individual thin-walled, UVtransparent microtubes, or in multiwell (e.g., 96 well) formats suitablefor high throughput procedures. Lyophilized Substrate has improvedlong-term stability compared to liquid solution in water or buffer. Ifprovided in liquid solution, stability is improved with storage at leastbelow −20° C., such as at −80° C. Storage in individual aliquots limitspotential for contamination with environmental ribonucleases.Alternatively, the Substrate can be provided in bulk, either lyophilizedor in liquid solution. Alternatively, substrate can be provided in bulkand can be dispersed at the discretion of the user.

An additional kit of the invention includes a set of enzyme-specific orenzyme-selective Substrates that together detect most RNase activitiesand individually can be used to distinguish between differentribonuclease enzymes. Such a kit can be used to assess the nature andsource of RNase contamination or can measure activity of specific enzymeof interest.

In Vitro Assays for Evaluating Nuclease Activity

In certain embodiments, the present invention provides in vitro assaysfor evaluating the activity of microbial nucleases on various nucleicacid substrates. In certain embodiments the assay evaluates the activityof mycoplasma nucleases. In certain embodiments the assay evaluates theactivity of Staphylococcus aureus or Streptococcus pneumoniae nucleases.For example, a biological sample (e.g., tissue, cells, biologicalfluids) or material derived from such a sample is combined with anoligonucleotide-based probe and incubated for a period to time. Thefluorescence level of this reaction is then measured (e.g., with afluorometer), and compared with the fluorescence levels of similarreactions that serve as positive and negative controls.

Example 1

Degradation of Nuclease-Stabilized RNA Oligonucleotides inMycoplasma-Contaminated Cell Culture Media

Artificial RNA reagents such as siRNAs and aptamers often must bechemically modified for optimal effectiveness in environments thatinclude ribonucleases. Mycoplasmas are common bacterial contaminants ofmammalian cell cultures that are known to produce ribonucleases. Here,the inventors describe the rapid degradation of nuclease-stabilized RNAoligonucleotides in an HEK cell culture contaminated with Mycoplasmafermentans, a common species of mycoplasma. RNA with 2′-fluoro- or2′-O-methyl-modified pyrimidines was readily degraded in conditionedmedia from this culture, but was stable in conditioned media fromuncontaminated HEK cells. RNA completely modified with 2′-O-methyls wasnot degraded in the mycoplasma contaminated media. RNA zymogram analysisof conditioned culture media and material centrifuged from the mediarevealed several distinct protein bands (ranging from 30 to 68 kDa)capable of degrading RNA with 2′-fluoro- or 2′-O-methyl-modifiedpyrimidines. Finally, the mycoplasma-associated nuclease was detected inmaterial centrifuged from the contaminated culture supernatants in aslittle as 15 minutes with an RNA oligo containing 2′-O-methyl-modifiedpyrimidines and labeled with a 5′-FAM and 3′-quencher. These resultssuggest that mycoplasma contamination may be a critical confoundingvariable for cell culture experiments involving RNA-based reagents, withparticular relevance for applications involving naked RNA (e.g.,aptamer-siRNA chimeras).

Synthetic RNA that is exposed to cells or tissues must be protected fromribonuclease degradation in order to carry out its intended function inmost cases. Common approaches for avoiding nuclease degradation includenanoparticle encapsulation which insulates the RNA from exposure toribonucleases and chemical modification to render it resistant todegradation. Modification of RNA by substituting O-methyl or fluorogroups for the hydroxyl at the 2′-position of the ribose can greatlyenhance its stability in the presence of extracellular mammalianribonucleases.

These modifications are widely employed in the development of siRNAs andRNA aptamers for both research and therapeutic applications. siRNAs canbe modified with 2′-O-methyl substitutions in both sense and antisensestrands without loss of silencing potency, but only a subset ofnucleotides are typically modified with 2′-O-methyls asover-modification of the siRNA can reduce or eliminate its silencingability. siRNAs with 2′-fluoro modified pyrimidines have also beenreported to retain silencing activity in vitro as well as in vivo.

RNA with 2′-fluoro modified pyrimidines is the most commonly usedchemistry for development of RNA aptamers with potential therapeuticapplications. Such RNA is stable in animal serum and can also beefficiently transcribed in vitro with a mutant viral RNA polymerase,thus facilitating its use in the aptamer discovery process known asSELEX (Systematic Evolution of Ligands by EXpontential enrichment). Thestability of this RNA in other contexts such as conditioned cell culturemedia has not been well-studied.

Mycoplasmas are a genus of small bacteria that are common contaminantsof cell cultures. They lack a cell wall, are not susceptible to theantibiotics usually employed in cell culture and often go undetected incell culture due to their small size. Some mycoplasma species, notablyMycoplasma pneumoniae, are human pathogens. Various mycoplasma speciesare known to produce ribonucleases and deoxyribonucleases; however, theability of these nucleases to degrade chemically modified RNAformulations has not been explored prior to the present work.

The inventors evaluated the stability of RNA with 2′-fluoro modifiedpyrimidines in cell culture media conditioned by human embryonic kidney293 (HEK) cells and found the RNA to be substantially degraded afterfairly brief incubations. It was subsequently determined that the HEKcells were contaminated with mycoplasma, and it was investigated whetherthis contamination was responsible for the observed nuclease activity.

Materials and Methods

Cell Culture and Conditioned Media.

HEK cells were inadvertently contaminated with mycoplasma at some pointduring routine culture maintenance. The contamination was later detectedand confirmed by PCR to be Mycoplasma fermentans. This mycoplasmacontaminated cell line was used as a positive control for mycoplasmatesting methods. Uncontaminated HEK cells were obtained from ATCC(ATCC-CRL-1573™). Contaminated and uncontaminated HEK cells were grownin DMEM (GIBCO) containing 10% heat-inactivated bovine serum, 50 U/mlpenicillin, and 50 μg/ml streptomycin at 37° C., 5% CO₂ in a moistatmosphere. For preparation of conditioned media, contaminated oruncontaminated HEK cells were grown to ˜80% confluency on 100 mm or 150mm culture dishes. The culture media was then replaced with fresh media.After 48 hours of incubation, the media was centrifuged for 6 minutes at1,250 rpm in a table-top centrifuge to remove cellular debris. Finally,the supernatant was transferred into a fresh tube and used as“conditioned media.” Unconditioned media had the same composition (seeabove), but was not incubated with cells. Particulate matter wascentrifuged from such conditioned media for the experiments described inFIG. 1C. 6 milliliters of conditioned media was centrifuged at 13,300rpm in a microcentrifuge. The pellet was washed with PBS and thendissolved in 20 μl 1% Triton X-100 in PBS. Eppendorf tubes with thesereactions were imaged with a digital camera and UV-lighttrans-illumination.

Mycoplasma Culture.

Mycoplasma broth consisted of 10% yeast extract solution (Gibco), 20%heat-inactivated fetal bovine serum, 70% heart infusion broth (BDBiosciences), 50 U/ml penicillin, and 50 pg/ml streptomycin. Afreeze-dried culture of Mycoplasma fermentans (ATCC#15474) wasrehydrated in 10 ml of mycoplasma broth. Several 10-fold serialdilutions of this culture were then prepared and the bacteria were grownin 50 ml conical tubes at 37° C. for several days. For the experimentshown in FIG. 2, 1 ml of Mycoplasma fermentans culture grown for 5 dayswas pelleted at 13,3000 rpms for 5 minutes. Supernatant was discardedand the lysate was prepared by dissolving the pellet in 20 μl 1% TritonX-100 in PBS. The lysate was incubated with RNAse substrates for 1 hourat 37° C.

Chemically Modified RNA.

The following 51 nucleotide long RNA sequence was used for the gel-baseddegradation assays and the RNA zymograms:5′-GGGAGGACGAUGCGGGACUAGCGAUCUGUUACGCACAGACGACUCGCCCGA-3′. Severalversions of this RNA, with modifications as described in figure legendsand the results section were used. FAM (fluorescein amidite)-labeledversions were used in the gel-based degradation assays, whereasnon-fluorescent versions were used for the zymograms. These RNAs wereobtained from Trilink Biotechnologies (San Diego, Calif.).

Gel-Based Degradation Assay.

For each degradation assay sample, 6 μl of oligo (2 μM) was combinedwith 6 μl of unconditioned and conditioned media and incubated for 0.5,1, 2, or 4 hours at 37° C. After incubation, samples were combined with141 of loading buffer (formamide with 0.5×TBE), incubated for 6 minutesat 65° C., transferred to ice for 5 minutes, briefly centrifuged andkept on ice until loading. Samples were run on a 7.7 M Urea/10%acrylamide gel at 100 volts for 80 minutes. Gel images were acquiredwith a Gel Doc™ XR+ System (Bio-Rad) with ultraviolet lighttransillumination and a standard fluorescence filter for imagingethidium bromide.

RNAse Substrate Plate-Reader Assays.

The RNAse substrates were synthesized by Integrated DNA Technologies(IDT; Coralville, Iowa). These probes consist of a 12 nucleotide longRNA oligo, 5′-UCUCGUACGUUC-3′, with the chemical modifications indicatedin figure legends, flanked by a FAM (5′-modification) and a pair offluorescence quenchers, “ZEN” and “Iowa Black” (3′-modifications). Forthe RNA degradation assays, 1 μl of each RNAse substrate (50 picomoles)was combined with 9 μl of sample (e.g., conditioned media) and incubatedat 37° C. for time points indicated in the figures. After the incubationperiod, 290 μl of PBS supplemented with 10 mM EDTA and 10 mM EGTA wasadded to each sample and 95 μl of each sample was loaded in triplicateinto a 96-well plate (96F non-treated black microwell plate (NUNC)).Fluorescence intensity was measured with a fluorescence microplatereader (Analyst HT; Biosystems). For the Triton X-100 lysate samples,the undiluted 10 μl reactions were imaged in eppendorf tubes with a GelDoc™ XR+ System (Bio-Rad) with ultraviolet light transillumination and astandard fluorescence filter for imaging ethidium bromide.

PCR.

All cell cultures were tested for mycoplasma infection by PCR. Fourprimer sets, previously described (Choppa, P. C., Vojdani, A., Tagle,C., Andrin, R., and Magtoto, L. (1998). Multiplex PCR for the detectionof Mycoplasma fermentans, M. hominis and M. penetrans in cell culturesand blood samples of patients with chronic fatigue syndrome. Mol CellProbes 12, 301-308), were used to identify a conserved region among allmembers of the genus mycoplasma and three specific species: Mycoplasmafermentans, Mycoplasma hominis and Mycoplasma penetrans. Mycoplasma,centrifuged from conditioned cell culture media, provided the templateDNA for the mycoplasma specific PCRs. The mycoplasma was isolated fromthe culture media as follows: conditioned media was centrifuged for 6minutes at 1,250 rpm to pellet cellular debris. 2 ml of the supernatantfrom this spin were then centrifuged for 5 minutes at 17,000×g to pelletany mycoplasma present in the media. The pellet was re-suspended in 500of water; this served as the PCR template. The PCR reaction mixtureswere prepared in a total volume of 100 μl containing 10 μl of PCRtemplate, 2 μl dNTP's (10 μM), 1 μl of each primer (100 μM), 50 μl ofChoice Taq Mastermix (Denville Scientific) and 36 μl of water. 30 cyclesof PCR were carried out. The temperature steps were as follows: 94° C.for 5 minutes, 30× (denaturation at 94° C. for 30 seconds; annealing at55° C. for 30 seconds; elongation at 72° C. for 30 seconds) a finalextension step of 72° C. for 10 minutes was carried out at thecompletion of the cycling. The PCR products were analyzed on a 2% (w/v)agarose gel stained with 0.5 μg/ml ethidium bromide. The DNA bands werevisualized with a Gel Doc™ XR+ System (Bio-Rad) with ultraviolet lighttransillumination and a standard fluorescence filter for imagingethidium bromide.

DAPI Staining.

Mycoplasma was visualized in cultured cells via DAPI(4′,6-diamidino-2-phenylindole, dihydrochloride, Invitrogen) staining.Briefly, HEK cells were grown on glass bottomed culture dishes fromMatTek (Ashland, Mass.). Cells were then fixed by incubation for 20minutes at −20° C. in 100% methanol and stained with DAPI following theprotocol provided in the DAPI product insert. The cells were then rinsedseveral times in PBS and fluorescence was visualized with an OlympusIX71 fluorescence microscope equipped with a 40× oil-immersionobjective, fluorescence filters appropriate for DAPI and a cooled CCDdigital camera.

DNA Zymograms.

Mycoplasma-free and mycoplasma-positive cell cultures were serum-starvedfor 48 hours on 150 mm culture dishes in 20 ml of DMEM. Media wascollected, spun at 1,250 rpms for 6 minutes to eliminate cell debris,then spun at 17,000×g for 5 minutes to pellet mycoplasma from theconditioned media. These pellets were solubilized in 50 μl SDS sampleloading buffer. The supernatants from the second centrifugation wereconcentrated with a YM-10 Amicon centrifugal filter device (MW cutoff of10 kDa) to a final volume of approximately 100 μl. One or 3 μl of theconcentrated media or pellet, respectively, were loaded per lane of an8% acrylamide SDS gel containing 200 μg/ml salmon sperm DNA(Invitrogen). After the gel was run, nucleases were activated by aseries of 10 minute washes: 2 washes in 2 mM CaCl₂, 2 mM MgCl₂, 2.5%Triton X-100 in water; 2 washes in 2 mM CaCl₂, 2 mM MgCl₂, 2.5% TritonX-100 in 50 mM Tris-HCl (pH 7.4); 2 washes in 2 mM CaCl₂, 2 mM MgCl₂ in50 mM Tris-HCl (pH 7.4). The gels were then incubated in 2 mM CaCl₂, 2mM MgCl₂ in 50 mM Tris-HCl (pH 7.4) for either 2 hours or overnight at37° C. The gels were stained with 0.5 μg/ml ethidium bromide andvisualized with a Gel Doc™ XR+ System (Bio-Rad) with ultraviolet lighttransillumination and a standard fluorescence filter for imagingethidium bromide.

Chemically Modified RNA Zymograms.

Samples were prepared as for the DNA zymograms (described above).Proteins were separated on 8% acrylamide SDS gels polymerized witheither 550 nM of an RNA oligo with 2′-fluoro-modified pyrimidines or 250nM of an RNA oligo with 2′-O-methyl-modified pyrimidines. See“Chemically Modified RNA” above for the sequence of these oligos. Gelswere washed as above, but stained with a 1:10,000 dilution of Sybr Goldnucleic acid gel stain (Invitrogen) and visualized with a Gel Doc™ XR+System (Bio-Rad) with ultraviolet light transillumination and a standardfluorescence filter for imaging ethidium bromide.

Results

To evaluate the stability of RNA with 2′-fluoro modified pyrimidines inconditioned culture media, a 51 nucleotide RNA with 2′-fluoro modifiedpyrimidines (underlined) and a 3′-FAM(5′-GGGAGGACGAUGCGGGACUAGCGAUCUGUUACGCACAGACGACUCGCCCGA-3′-FAM) wasincubated in serum-containing media, conditioned with an HEK cellculture recently obtained from ATCC, or with an older HEK cell culture.As previously reported, this RNA was found to be resistant to nucleasedegradation in the presence of animal serum. While the modified RNA wasalso stable in conditioned media from the HEK cells obtained from ATCC,the conditioned media from the older HEK cells almost completelydegraded it after a 4-hour incubation at 37° C. The RNA was thenresolved on a urea/acrylamide denaturing gel and imaged with a digitalcamera and UV-light trans-illumination; the oligo was labeled on its3′-end with FAM. PCR primer sets specific for genomic components ofMycoplasma fermentans, Mycoplasma hominis, Mycoplasma penetrans, or fora region of the mycoplasma genome that is conserved within the genus,were used to amplify DNA present in conditioned culture media. ExpectedPCR product sizes are as follows: mycoplasma genus PCR: 280 bp;Mycoplasma fermentans: 206 bp; Mycoplasma hominis: 170 bp; Mycoplasmapenetrans: 470 bp. The PCR assay for the presence of mycoplasma detecteda DNA sequence conserved within the genome of the mycoplasma genus inthe culture supernatant of the older HEK cell culture supernatant, butnot in the media from the more recently obtained culture. A DNA sequencespecific to the Mycoplasma fermentans species was also detected in mediafrom the older HEK cell culture, as indicated with a PCR product ofexpected size. Sequencing of this PCR product confirmed that theamplified sequence is derived from the Mycoplasma fermentans genome. Incontrast, neither Mycoplasma hominis nor Mycoplasma penetrans wasdetected.

As an additional means of detecting mycoplasma, DAPI staining of HEKcells from these two cultures was carried out. Small, punctate,extra-nuclear DAPI-labeling, indicative of mycoplasma contamination, wasseen throughout the older HEK culture, but only nuclear labeling wasseen in the culture obtained from ATCC. Together, these data demonstratethe presence of a ribonuclease that readily degrades RNA with 2′-fluoromodified pyrimidines in a mycoplasma-contaminated but not in amycoplasma-free HEK cell culture.

Next, the activity of this ribonuclease after heat pre-treatment wasstudied, in the presence of EDTA (a chelator of divalent cations) and inthe presence of a broad-spectrum ribonuclease inhibitor. The same RNAoligo initially examined was used for this experiment (51-mer with2′-fluoro-modified pyrimidines and a 3′-FAM) with conditioned media fromthe mycoplasma-contaminated HEK cells. Results of this experimentindicate that the ribonuclease activity is sensitive to heat treatmentand is thus likely protein in nature. Like many ribonucleases, itsactivity is dependent on divalent cations as chelation of divalentcations with EDTA inhibited degradation of the modified RNA. Todetermine the dependence of the nuclease activity on divalent cations,conditioned media was incubated with RNA in the presence of 10 mM EDTA.A broad-spectrum RNAse inhibitor, Superase.in, was co-incubated (at 1unit/μl) with the RNA in conditioned media to determine the sensitivityof the nuclease activity to this reagent. The RNA was resolved on aurea/acrylamide denaturing gel and imaged with a digital camera andUV-light trans-illumination; the oligo is labeled on its 3′-end withFAM. The broad-spectrum RNAse inhibitor, Superase.in, did not have anapparent impact on the activity.

While the 2′-fluoro nucleotide modification is widely used for thedevelopment of RNA aptamer-based therapeutic approaches, othermodifications are more commonly used to protect synthetic RNAs in otherapplications such as RNAi. The 2′-O-methyl modification is widelyemployed and we thus examined the susceptibility of RNA with2′-O-methyl-modified nucleotides to degradation by themycoplasma-associated ribonuclease activity. For this experiment, 3 RNAoligos were used. Each was 51 nucleotides in length, of identicalsequence and with a 3′-FAM. The first oligo had 2′-fluoro-modifiedpyrimidines (purines were unmodified) (described above), the second had2′-O-methyl-modified pyrimidines (purines were unmodified) and everynucleotide of the third oligo was modified with 2′-O-methyls.Co-incubation of these oligos with media conditioned by themycoplasma-contaminated HEK cells for 30 minutes, 1 hour, 2 hours or 4hours again demonstrated the near-complete degradation of the oligo with2′-fluoro-modified pyrimidines. The oligo with 2′-O-methyl-modifiedpyrimidines was more resistant to degradation, but was almost completelydegraded after 4 hours. Finally, there was no detectable degradation ofthe oligo that was completely modified with 2′-O-methyls at any of thetime-points.

Additional cell lines, contaminated with distinct mycoplasma species(i.e., non-Mycoplasma fermentans species) were also tested for nucleaseactivity against RNA oligos with 2′-O-methyl- and 2′-fluoro-modifiedpyrimidines. Some of these cell lines possessed strong nuclease activityin their supernatants while others did not.

To further characterize the mycoplasma-associated ribonuclease,zymograms were carried out with unmodified DNA or RNA with 2′-fluoro- or2′-O-methyl-modified pyrimidines. For these experiments, serum-freeconditioned cell culture media was used that was concentrated withfilter centrifugation as well as detergent-lysed particulate mattercentrifuged from the conditioned media. Concentrated media or materialpelleted by centrifugation from media conditioned by mycoplasma-free ormycoplasma contaminated HEK cells was resolved on 8% acrylamide SDS gelsembedded with DNA, RNA with 2′-fluoro-modified pyrimidines or RNA with2′-O-methyl-modified pyrimidines. After running, the gels were washedwith SDS-free buffer containing divalent cations and incubated at 37° C.for 2 hours to allow nuclease digestion. The gels were stained withethidium bromide (DNA zymogram) or SYBR Gold nucleic acid gel stain andimaged with a digital camera and UV-light trans-illumination, revealingprotein bands with nuclease activity. The particulate matter presumablycontains mycoplasma in the contaminated culture sample and was alsofound to possess ribonuclease activity.

Multiple protein bands present in the mycoplasma-contaminated, but notthe mycoplasma-free concentrated culture supernatants could be seen inall 3 zymograms. A cluster of bands that migrated between the 37 and 50kDa molecular weight markers was prominent in these samples. A smallerprotein, of approximately 30 kDa digested the modified RNAs; nodigestion was seen in this region of the DNA zymogram. A larger protein,of approximately 68 kDa, produced a band in the DNA zymogram, but not inthe modified RNA zymograms. However, longer digestion periods (e.g.,overnight) did yield a band of approximately this size in the modifiedRNA zymograms. The prominent cluster of bands between 37 kDa and 50 kDapresent in all of the zymograms suggests the presence of multiplenucleases with broad substrate specificities.

The detergent-lysed particulate matter produced a very different patternof bands on the zymograms. As with the concentrated supernatant, darkbands indicating digestion were only seen in the sample prepared fromthe mycoplasma-contaminated culture. However, the patterns of bandsclearly indicate that there are multiple nucleases present in theparticulate matter of the culture media with distinct substratespecificities. The prominent cluster of bands between the 37 kDa and 50kDa molecular weight markers that was present in the concentratedculture supernatant was not seen in the particulate matter samples.

Because the mycoplasma-associated nuclease can be distinguished fromendogenous mammalian nucleases by its distinct substrate specificity, wereasoned that the presence of mycoplasmas, in various contexts, might beinferred by the susceptibility of chemically modified ribonucleasesubstrates to degradation. While gel-based assays provide a simple andstraightforward means of detecting nuclease activity, a more rapid andsensitive assay for ribonucleases that degrade unmodified RNA has beendescribed. The basis for this assay is a short oligonucleotide RNAsesubstrate, end-labeled with a fluorophore on one end that is renderednon-fluorescent by its close proximity to a quencher on the other end(FIG. 1A) (Kelemen, B. R., et al. (1999). Hypersensitive substrate forribonucleases. Nucleic Acids Res 27, 3696-3701). Upon cleavage of thesubstrate, the quencher diffuses away from the fluorophore, which thenexhibits fluorescence.

This approach was adapted to detect the mycoplasma-associated nucleaseby generating chemically modified RNAse substrates with fluorophore andquencher conjugates. Four different RNA chemistries were tested:2′-fluoro-modified pyrimidines, 2′-O-methyl-modified pyrimidines,complete 2′-fluoro modifications, and complete 2′-O-methylmodifications. Initially, each of these RNAse substrates was incubatedfor 4 hours with culture media conditioned by either mycoplasma-free ormycoplasma-contaminated HEK cells (FIG. 1B). While the complete2′-O-methyl-modified substrate was not digested in either media, theother 3 RNAse substrates exhibited substantially greater fluorescenceafter incubation in the mycoplasma-contaminated media. Of these, thesubstrate with 2′-O-methyl-modified pyrimidines exhibited the greatestrelative fluorescence increase between uncontaminated and contaminatedmedia. This substrate was thus characterized further.

Centrifugation of particulate matter from the mycoplasma-contaminatedculture supernatants provided a simple and rapid means of obtainingconcentrated nuclease activity. The possibility that this approach mightincrease the sensitivity of mycoplasma detection with RNAse substrateswas explored. The RNAse substrate with 2′-O-methyl-modified pyrimidineswas incubated with a detergent lysate of centrifuged particulate matterfrom mycoplasma-free or mycoplasma-contaminated HEK cells for 1 hour(FIG. 1C). Conditioned media from these cultures was compared inparallel. While both the lysate and conditioned media exhibited strongnuclease activity, the lysate produced a greater signal in this assay. Aclear signal could be seen over the background in this assay, even withan abbreviated (15 minutes) incubation (fluorescence was measured on anultraviolet light box in this case).

The contaminated HEK cell culture is a complex preparation as itcontains cells derived from two distinct organisms. While theuncontaminated HEK cells lack nuclease activity capable of efficientlydegrading RNA with 2′-fluoro-modified or 2′-O-methyl-modifiedpyrimidines, we also sought to measure such activity in a pure cultureof Mycoplasma fermentans. Consistent with the current observations ofthe contaminated HEK cell culture, lysates prepared from Mycoplasmafermentans bacteria exhibited robust nuclease activity against RNAsubstrates with 2′-fluoro-modified and 2′-O-methyl modified pyrimidines(FIG. 2). Nuclease activity against RNA substrates with2′-fluoro-modified and 2′-O-methyl-modified pyrimidines was also foundin the bacterial culture supernatant (not shown).

Discussion

It was found that conditioned media from HEK cells contaminated withMycoplasma fermentans possesses ribonuclease activity that readilydegrades RNA with 2′-fluoro-modified pyrimidines and2′-O-methyl-modified pyrimidines. Comparable ribonuclease activity wasseen in a pure culture of Mycoplasma fermentans, but not in anuncontaminated, HEK cell culture. These observations are consistent withthe conclusion that the activity in the contaminated HEK cell culture isderived from the mycoplasma bacteria. Zymograms with chemically modifiedRNA revealed the presence of multiple protein bands (from ˜30 kDa to ˜68kDa) in the conditioned, mycoplasma-contaminated culture media thatpossess this ribonuclease activity. Some of these proteins were found inparticulate matter in the media, presumably containing free-floatingmycoplasma. RNAse substrates synthesized with chemically modified RNAdetected the presence of this ribonuclease activity after a 15 minuteincubation.

This work was undertaken to better understand the stability ofchemically modified RNA oligonucleotides in cell culture settings. Theresults identify a critical variable for the use of RNA-based reagentsin cell culture experiments. While the potential for mycoplasma-basedartifacts in cell culture experiments is widely known, many researchersdo not regularly test their cell lines for mycoplasmas. Lack of regulartesting is perhaps the primary reason that mycoplasmas continue to beproblematic for cell culture studies. It is estimated that 15-35% ofcell lines used are contaminated with mycoplasmas, with MycoplasmaFermentans among the most prevalent species identified in cell lines.

The manner in which mycoplasma contamination affects experimentaloutcome varies depending on the nature of the experiment. The presentresults suggest that experiments involving the application of naked RNAdirectly to cells are particularly vulnerable to mycoplasma-dependentRNA degradation and experimental failure. These experiments include thestudy or application of siRNAs, RNA aptamers and ribozymes. Forinstance, the delivery of siRNAs by directly coupling them to targetingreagents such as antibodies, aptamers, peptides and other syntheticligands all entail the application of naked RNA to cells. The evaluationof RNA aptamers targeting cell surface receptors or extracellulartargets such as growth factors in cell culture, likewise, involves theapplication of naked RNA to cells.

The characterization of the mycoplasma-associated ribonuclease activitywith nucleic acid zymograms revealed the presence of multiple proteinswith deoxyribonuclease and ribonuclease activity in the contaminatedcell culture media. The presence of multiple bands in similar patternsin all 3 of the zymograms between the 37 kDa and 50 kDa molecular weightmarkers suggests that several nucleases capable of digesting DNA, or RNAwith 2′-fluoro- or 2′-O-methyl-modified pyrimidines are produced by themycoplasma. Other bands found in the mycoplasma-contaminated samplesexhibited substrate specific degradation among the 3 nucleic acidchemistries tested. Altogether, the results from the zymograms suggestthere are multiple mycoplasma-derived ribonucleases present in thecontaminated culture media that can readily degrade RNA with either2′-fluoro- or 2′-O-methyl-modified pyrimidines. The identity of theseproteins has not been determined. Because zymograms depend on proteinrefolding following SDS-denaturation, it is possible that someribonucleases present in the culture media did not yield a signal on thezymograms.

The fraction of mycoplasma species that produce ribonucleases capable ofdegrading chemically modified RNAs is uncertain. The fact that RNAoligos with 2′-fluoro- or 2′-O-methyl-modified pyrimidines were degradedin cultures contaminated with distinct, yet unidentified species ofmycoplasma indicates that the activity is not limited to the Mycoplasmafermentans species. Considering the diverse nature of mycoplasmas, it isperhaps not surprising that mycoplasma-contaminated cell cultures thatlacked such robust nuclease activity were found.

Because many mycoplasmas are human pathogens, the detection ofmycoplasma-derived nucleases has clinical diagnostic applications. DNAseactivity has in fact been used to differentiate among various bacterialpathogens, including the identification of coagulase-positivestaphylococci, such as Staphylococcus aureus in bovine milk samples.Such assays depend on the isolation of the bacteria from biologicalfluids and tissues that also contain DNAses, which would otherwisegenerate background; isolation and culture of the bacteria can consumevaluable time. The use of chemically modified nucleic acids provides analternative that could be used in more clinically relevant settingswithout generating background. Indeed, a chemically modified RNAsesubstrate that rapidly and robustly detected mycoplasma-derivedribonuclease activity in serum-containing conditioned media wasdeveloped; digestion of this RNAse substrate in the same mediaconditioned by an uncontaminated culture was minimal. Chemicallymodified nucleic acids can thus facilitate the rapid determination ofthe presence of bacterial contamination.

Example 2 In Vivo Detection

The cleavage of oligonucleotides can be visualized in various ways, butas discussed above, the inventors favor flanking the sequences with afluorophore and a quencher for rapid detection of the cleavage activitywith a fluorometer. Advancing one step further, the inventors envisioninjecting the fluorescent probe into patients and using fluorescentdetection to localize sights of infection (in addition to specificpathogen data) clearly within the patient. Preliminary data of this typehas been established in mouse models. Briefly, mice were injected withmicrococcal nuclease (purified Staph. aureus nuclease) in leg andinjected with probe in tail vein. This procedure resulted influorescence being seen at site of nuclease and subsequently in liver.

Example 3 In Vitro Detection

Nuclease Probe Plate-Reader Assay:

The nuclease probes were synthesized by Integrated DNA Technologies(IDT; Coralville, Iowa). These probes consist of a 12 nucleotide longRNA oligo, 5′-UCUCGUACGUUC-3′, with the chemical modifications, flankedby a FAM (5′-modification) and a pair of fluorescence quenchers, “ZEN”and “Iowa Black” (3′-modifications. Three samples were assayed fordegradation. PBS, 1 μl of each probe (50 picomoles) was combined with 9μl of PBS. RNase A, 1 μl of each probe was combined with 8 μl of PBS and1 μl RNase A (˜50 U/μl). Micrococcal Nuclease (MN), 1 μl of each probewas combined with 8 μl of PBS and 1 μl of MN (10 U/μl). All the sampleswere incubated at 37° C. for 4 hours. After the incubation period, 290μl of PBS supplemented with 10 mM EDTA and 10 mM EGTA was added to eachsample and 95 μl of each sample was loaded in triplicate into a 96-wellplate (96F non-treated black microwell plate (NUNC)). Fluorescencelevels are shown in FIG. 2 (these are the PMT (photomultiplier tube)values). Fluorescence was measured with a fluorometer.

A nuclease from a third pathogenic bacterium, Streptococcus pneumoniae,has also been evaluated. A nuclease is expressed on the membrane of theStreptococcus pneumoniae bacterium, making it easier to detect thannucleases that are secreted because it cannot diffuse away from thecell. The investigators found that this nuclease, which is known as EndAis capable of digesting a probe that has 2′-fluoro modified pyrimidines,but not a probe with 2′-O-methyl modified pyrimidines.

Degradation activity of Micrococcal Nuclease and EndA Nuclease.

Unmodified (RNA and DNA) and modified (2′-Fluoro pyrimidines and2′-O-Methyl pyrimidines) nucleic acid substrates were used to assay thenuclease activity profile of Micrococcal Nuclease (MN) and EndA (H160G)Nuclease. The substrates were flanked by a fluorescent dye (FAM) at the5′-end and a quencher at the 3′-end. This approach allows the evaluationof nuclease activity which is indicated by increases in fluorescenceupon substrate digestion. 50 pmoles of substrate were incubated with MN(1 U/μL) and EndA H160G Nuclease (2 μM) in 10 μl total volume. Imadazolewas included in the EndA H160G reactions to recapitulate the enzymaticproperties of the wildtype enzyme. This mutant version of the enzyme wasused because the wt enzyme was toxic to E. coli and could not beproduced recombinantly in large amounts. 50 pmoles of each substrate andbuffer were used as controls. All reactions were incubated for 30minutes at 37° C. After incubation, 290 μl of buffer supplemented with10 mM EDTA and 10 mM EGTA were added to each sample and 95 μl of eachsample were loaded in triplicate into a 96-well plate (96F non-treatedblack microwell plate (NUNC)). Fluorescence intensity was measured witha fluorescence microplate reader (Analyst HT; Biosystems) (FIG. 3).

Example 4 Nuclease-Activated Probes for Imaging Staphylococcus aureusInfections

S. aureus infections are a major clinical problem that results in avariety of life-threatening and debilitating medical conditionsincluding septic joints, osteomyelitis and endocarditis. Development ofantibiotic resistant strains of S. aureus has compounded the difficultyof treating infections and highlights the need for novel antibiotics andbetter diagnostic approaches for their evaluation. Most S. aureusinfections with clinical significance are localized to internal tissuesor organs that are difficult to access. Definitive diagnosis of S.aureus infection thus necessitates testing biopsies of suspected tissuesfor presence of the bacteria. Because only limited tissues can besurveyed, biopsies offer only a limited assessment of the possibility anindividual is suffering from an S. aureus infection. In some cases, suchas endocarditis, biopsies are impractical and diagnoses are made withcircumstantial evidence such as heart murmur and the detection ofbacteria in the circulation.

To address the present shortcomings in the diagnostic technology forlocalized S. aureus (and other bacterial) infections, molecular imagingapproaches have been developed to non-invasively detect bacteria inanimals. These approaches depend on the selective affinity of theimaging reagents for components of bacteria. For example, one approachuses molecular probes that function by binding components of bacteriawith greater affinity than mammalian cells and tissues. In general,because such probes are always “on” they have suboptimaltarget-to-background ratios, which limit their sensitivity. These probesare limited by the fact that they produce signal prior to encounteringtheir target (i.e., they are not activatable probes) and most of themare non-specific with respect to bacterial species.

An alternative molecular imaging approach, involving quenchedfluorescent probes that are activated by tumor-specific proteases, hasprovided a valuable imaging platform for cancer imaging. Because suchactivatable probes do not produce signal (fluorescence) until the probeencounters its target, the result is a very high target-to-backgroundratio and a much more sensitive means of target detection. While thisapproach has proven valuable for imaging cancer, to-date it has not beenapplied to imaging bacteria, possibly due to a scarcity of appropriatebacteria-derived proteases. The inventors exploited the interfacebetween chemically modified nucleic acids and bacterial nucleases todevelop activatable imaging probes for bacterial infections. Thisresearch is innovative because the exploitation of nucleases for imagingis a novel direction, both for the imaging of bacterial infections inparticular and for whole-animal imaging in general.

The present invention provides a robust activated imaging probe-basedapproach for the non-invasive detection and localization of S. aureusinfections in animals. This contribution is significant becauseactivated imaging probes have critical advantages (e.g., hightarget-to-background ratios) over existing technology for this problem,and may prove to be generally useful for both research and clinicaldiagnostic applications involving S. aureus. The present approachfacilitates the evaluation in experimental animals of novel antibioticsfor naturally occurring strains of these bacteria. This near-infraredfluorescence-based imaging approach also is useful for the diagnosis andtreatment evaluation of S. aureus infections in humans. Indeed,near-infrared fluorescent dyes are currently used as clinical imagingtools for retinal angiography, cardiac function, hepatic output,sentinel lymph node dissection and colon polyp identification. Theclinical applicability of near-infrared imaging, which has limitedimaging depth in tissues (estimated at 7-14 cm), is expanding due to thedevelopment of medical imaging devices such as endoscopes withfluorescence imaging capabilities. Interestingly, many additionalproblematic pathogens are also known to express secreted or cell-surfacenucleases (e.g., Streptococcus pneumoniae), which are used for theirdetection.

A. Generation of Nuclease-Activated Probes that Specifically DetectMicrococcal Nuclease (MN) of S. aureus

The need for clinical diagnostic imaging of bacterial infections isgreatest for localized infections, which are often difficult todiagnose. In contrast, systemic infections can usually be detected withsimple blood tests. S. aureus is the most common bacterial cause of avariety of focal infections in humans, including infectious joints,osteomyelitis and endocarditis. For example, S. aureus is the causativebacterial pathogen in approximately half of the cases of infectiousjoints which are a serious medical condition, associated withsubstantial morbidity and mortality. Additional types of bacteria thatare commonly found to cause septic joints include non-aureusStaphylococci and Streptococci (group A-G and pneumoniae). A variety ofadditional bacterial species, including Gram negative bacteria such ase. coli can also, in rare cases, cause septic joints.

Micrococcal nuclease is a robust extracellular nuclease produced by S.aureus. It readily digests DNA and RNA via endonuclease and exonucleaseactivities, and its activity has been used to detect the presence of S.aureus in various contexts for decades. MN has been found to play a rolein S. aureus immune evasion and is a virulence factor of S. aureus.Interestingly, a portion of MN is apparently expressed on the surface ofS. aureus cells.

Most Streptococcus species that cause infectious joints also produceextracellular nucleases. Group A Streptococci are known to produce atleast four such nucleases, SdaA, SdaB, SdaC and SdaD. Of these, SdaA andSdaC are known to be DNAses, while SdaB and SdaD are able to digest DNAand RNA (Wannamaker et al., 1967). SdaB and SdaD are thus expected todigest a more diverse set of chemically modified nucleic acids.Extracellular nucleases of Group B Streptococci have also been studiedand at least three of these enzymes degrade DNA and RNA (Ferrieri etal., 1980). DNAse activity has also been observed in culturesupernatants from Group C and G Streptococci, but the enzymesresponsible for this activity are not well-characterized. A cell-surfacenuclease of Streptococcus pneumoniae, known as EndA, has also beenwell-studied (Moon, A. F., Midon, M., Meiss, G., Pingoud, A., London, R.E., and Pedersen, L. C. (2011). Structural insights into catalytic andsubstrate binding mechanisms of the strategic EndA nuclease fromStreptococcus pneumoniae. Nucleic Acids Res 39, 2943-2953).

An ideal molecular imaging probe for S. aureus would produces a signalonly upon encountering the targeted, unmodified bacteria or materialderived from it. Such probes enable the in vivo dynamic imaging ofnaturally occurring S. aureus strains with superior target-to-backgroundratios over existing technologies and facilitate the clinical diagnosisand treatment evaluation of S. aureus infections in humans. The lack ofversatile, specific and robust bacterial imaging methods is a criticalbarrier for the study of S. aureus in animals and the evaluation of S.aureus infections in humans.

Oligonucleotide-based nuclease substrates with fluorophore-quencherpairs (fluorophore is unquenched upon nuclease digestion) are tailoredvia chemical modification to specifically detect nucleases of S. aureusand thus serve as specific and sensitive probes for the detection of thebacteria themselves. The data provided below demonstrate the sensitivedetection of an S. aureus-derived nuclease in vitro and in mice withchemically modified oligonucleotide-based nuclease substrates.Importantly, these substrates are resistant to mammalian nucleases; theythus exhibit a very low background in animals in the absence of foreignnucleases.

The data provide examples of chemically modified oligonucleotide probesthat can differentiate between MN and mammalian serum nucleases. Thus,oligonucleotides with the appropriate chemical modifications are readilydigested by MN, but resistant to both mammalian and various bacterialnucleases. Several distinct bacterial and mammalian nucleases have beentested in these in vitro experiments. These nuclease-activated probeswith quencher/fluorophore pairs (fluorophores will be near-infrared)that are susceptible to digestion by MN may enable the non-invasivedetection and localization of focal S. aureus infections in mice.

For therapeutic applications involving synthetic RNA, chemicalmodifications have been developed to increase the resistance of RNA todegradation by mammalian nucleases. Modification of pyrimidines bysubstitution of the 2′-OH of the ribose sugar for different groups suchas fluoro (2′-F) or O-methyl (2′-OMe) have been found to substantiallyincrease resistance of RNA to nuclease degradation (Green, L. S., et al.(1995). Nuclease-resistant nucleic acid ligands to vascular permeabilityfactor/vascular endothelial growth factor. Chem Biol 2, 683-695; Pieken,W. A., et al. (1991). Kinetic characterization of ribonuclease-resistant2′-modified hammerhead ribozymes. Science 253, 314-317). For example,RNA with 2′-F modified pyrimidines is stable is animal serum for manyhours. These modifications have become commonplace in the development ofRNA-based therapeutics (Behlke, M. A. (2008). Chemical modification ofsiRNAs for in vivo use. Oligonucleotides 18, 305-319; Thiel, K. W., andGiangrande, P. H. (2009). Therapeutic applications of DNA and RNAaptamers. Oligonucleotides 19, 209-222). Considering the stability ofthese modified RNAs in mammalian fluids, it was reasoned that they mightbe useful reagents for bacteria detection if bacteria-derived nucleasescan digest them. Thus, the ability of various bacterial nucleases(derived from S. aureus, Streptococcus pneumoniae and mycoplasma) todigest such modified RNA was measured.

To measure nuclease activity in vitro quenched fluorescent oligos wereused (platereader-based assays shown in FIG. 4A, B and C) andpolyacrylamide gel electrophoresis (PAGE, FIG. 1D). MN digestsunmodified RNA, RNA with pyrimidines modified with 2′-F, or 2′-OMe, orfully 2′-F or fully 2′-OMe modified RNA, whereas mammalian RNAse A onlydigests unmodified RNA (FIG. 4A). EndA (cell-surface nuclease ofStreptococcus pneumoniae) digests RNA with pyrimidines modified with2′-F, but not with 2′-OMe (FIG. 4B). EndA and MN thus have differentsubstrate specificities with respect to the modified RNAs, suggestingthat chemically modified RNA probes may be used to differentiate betweenthem. For detection of S. aureus via MN activity, culture supernatantsprovide a more clinically relevant preparation. Thus nuclease activityof S. aureus culture supernatants (wt and MN-negative (S. aureus MN-))was measured. The clear activity in the MN+ supernatant (DNA probe, FIG.4C) indicates that such probes can detect the presence of the bacteriavia MN activity. A PAGE-based assay, as shown in FIG. 4D for theactivity of a mycoplasma-derived nuclease, is a complement to theplatereader assay as it provides an assessment of the degradationproducts. Note the activity of the Mycoplasma fermentans-derivednuclease on the 2′-F and 2′-OMe (pyrimidines) modified RNA oligos.

Short oligonucleotides, flanked with a fluorophore (5′-end) and aquencher (3′-end) are useful reagents for evaluating the nucleasesusceptibility of oligos with many distinct nucleotide modifications. Totest the ability of nucleases derived from pathogenic bacteria todegrade oligonucleotides of different chemical compositions, thenucleases are co-incubated with such oligonucleotide probes, followed bymeasurement of fluorescence levels in a fluorescence plate reader.Increases in fluorescence beyond levels seen in control oligoincubations in which nucleases are omitted, are indications of oligodegradation. In addition to the simplicity and convenience of thisapproach, another advantage is that any probes found to specificallydetect MN in these assays can be used to instruct the design of in vivoprobes for S. aureus because the latter probes are also based on oligoswith quenched fluorophores. Oligonucleotide compositions found to bespecifically susceptible to degradation by MN are further studied byexamining the susceptibility of unlabeled (i.e., no fluorophore orquencher) versions of the oligonucleotides with polyacrylamide gelanalysis of degradation in place of the plate-reader assay.

The oligonucleotide probes consists of 12 nt-long RNA oligos(5′-UCUCGUACGUUC-3′) flanked by a FAM (5′-end) and fluorescencequenchers, “ZEN” and “Iowa Black” (3′-end). For the degradation assays,50 pmoles of each oligonucleotide are combined with each sample (e.g.,culture supernatant) and incubated at 37° C. for 30 minutes to 4 hours.The purified nucleases are diluted in PBS supplemented withphysiological concentrations of calcium and magnesium. Various dilutionsof each nuclease are tested to determine the limiting concentration ofeach. After incubations, the reactions are loaded in triplicate into a96-well plate. Fluorescence is measured with a microplate reader(Analyst HT; Biosystems). Controls for each experiment include anunmodified RNA probe incubated with buffer (−control) or RNAse A(+control). Each probe is incubated with buffer or culture broth only(to establish background fluorescence levels) in parallel with thenuclease incubations.

Chemical modifications that are tested include various modificationsthat are known to promote resistance to mammalian nucleases, including:2′-fluoro-β-D-arabinonucleotide (FANA), Locked Nucleic Acid (LNA),Unlocked Nucleic Acid (UNA), 2′-O-methyl, 2′-fluoro and phosphorothioate(a sugar-phosphate backbone modification) (Behlke, M. A. (2008).Chemical modification of siRNAs for in vivo use. Oligonucleotides 18,305-319).

Probes are also studied with the following gel-based degradation assayin order to determine the full extent of degradation. These experimentsare necessary to distinguish between enzymatic activity that mightsimply remove a terminal nucleotide or possibly the quencher orfluorophore from a probe as opposed to more thorough nuclease digestion.The former type of degradation may only occur with particularfluorophores or quenchers and thus may not be generally useful fornuclease detection. For each reaction, 50 pmoles of an unlabeled versionof the selected oligo is combined with buffer or with the nucleases,culture material or serum samples indicated above and incubated for 0.5to 4 hours at 37° C. After incubation, samples are resolved on a 7.7MUrea/10% acrylamide gel. Gel images (stained with SYBR Gold) areacquired with uv-light transillumination and a digital camera.

B. Demonstration of the Detection of the S. aureus Nuclease (MN) in Micewith Nuclease-Activated Probes.

Activatable imaging probes for non-invasive imaging of variousbiological phenomena, provide high target-to-background ratios, and arethus actively sought for applications such as cancer imaging. However,activatable imaging probes for focal bacterial infections have not beendescribed. The present experiments demonstrate the feasibility of anovel nucleic acid-based activatable imaging approach for the detectionand localization of S. aureus associated nuclease activity in mice.

The non-invasive detection of tumors in mice with quenched fluorescentprotease substrates was first reported in 1999 (Weissleder, R., et al.(1999). In vivo imaging of tumors with protease-activated near-infraredfluorescent probes. Nat Biotechnol 17, 375-378). These probes detectproteases that are overexpressed by cancer cells. Importantly, thefluorophores used in the probes absorb and emit near-infrared light,which can penetrate tissues much better than light in the visibleregions of the spectrum. The initial report of this approach providedthe conceptual basis for many subsequent studies describing similarprotease substrate-based tumor imaging approaches. Importantly, thisapproach is not limited to detection of subcutaneously implanted tumors.Bone metastases are among the types of cancers detectable withnear-infrared imaging. The activatable imaging probe concept has alsobeen pursued for non-invasive imaging in a variety of forms notinvolving protease. activation due to the high target-to-backgroundratios achieved with activatable probes.

Activatable molecular imaging approaches have not been developed forimaging bacterial infections. Instead, bacterial infections have beenimaged with probes that exhibit greater affinity for the bacteria thanfor mammalian cells and tissues. As the utility of NIR-based imaging forcancer became clearer, important progress has been made in developingmore sophisticated NIR-based imaging instrumentation, includingfluorescence tomography for acquisition of 3-dimensional fluorescenceimages and multispectral imaging approaches for removal ofautofluorescence and fluorescence multiplexing. NIR-based imagingtechnologies have also been introduced into clinical practice. While thedepth of light penetration with NIR light is a limitation of NIR-basedimaging (estimated to be 7-14 cm), the broad potential of the technologyin the clinic is highlighted by a recent study demonstrating thedeep-tissue imaging of lymphatic vessels within the leg of a humansubject.

Oligonucleotide-based probes with quenched fluorophores have been incommon use as tools for various molecular biology methods for over adecade. This robust technology includes Molecular Beacons and TaqManprobes whose fluorescence is unquenched after the probes anneal to atargeted complementary nucleic acid and “RNAse Substrates”, which areused to detect the presence of contaminating RNAses in laboratorysolutions.

For in vivo applicability of nuclease-activated imaging probes,visible-wavelength fluorophores (e.g., those used in FIGS. 4A-4D) arenot optimal due to high autofluorescence and light scattering of visiblelight by tissues. The inventors, therefore, tested nuclease-activatedprobes with an NIR fluorophore (Cy5.5). A 2′-fluoro pyrimidine modifiedRNA oligo with 5′-Cy5.5 and 3′-quencer were combined with PBS alone orPBS plus micrococcal nuclease and incubated for 60 minutes at 37° C.prior to imaging. Fluorescence was measured with a Xenogen IVIS smallanimal imaging system. A quenched Cy5.5 probe composed of RNA with 2′-Fmodified pyrimidines exhibited a very low level of NIR fluorescenceprior to digestion, and a robust (130-fold) increase in fluorescenceafter MN digestion. To explore the utility of this probe for imagingbacterial nucleases in mice, MN was injected into the leg muscle of amouse which was subsequently administered 5 nmoles of the probe via tailvein injection. Fluorescence was found to develop initially at the siteof MN injection. This signal increased over the next 45 minutes. Inaddition, a strong fluorescence signal developed in the abdomen,presumably emanating from the liver. Whether this liver-based signalresulted from liver-based digestion of the probe or accumulation ofprobe fragments of the MN digestion is uncertain. Finally, to evaluatethe utility of luciferase-expressing S. aureus for multimodal mouseimaging experiments with Cy5.5-labeled probes, a Lux operon wastransferred to the Newman strain of S. aureus and imaged withbioluminescence and Cy5.5 fluorescence channels of an IVIS system. Whilethe bioluminescence of the Luc+ S. aureus was strong, theluciferase-derived light was not seen in the Cy5.5 fluorescence channel,thus indicating the feasibility of Luciferase/Cy5.5 co-localizationexperiments (i.e., the Luciferase signal does not interfere with Cy5.5measurements).

To evaluate the ability of quenched fluorescent nuclease substrates toindicate the presence and localization of focal S. aureus infections inmice, we will use a probe that yielded promising results in preliminarywhole animal optical imaging experiments. This probe, which consists ofa short RNA oligonucleotide with 2′-F modified pyrimidines andunmodified purines, is resistant to activation by mammalian nucleases,but susceptible to degradation (and activation) by various bacterialnucleases, including nucleases produced by S. aureus (MN), Streptococcuspneumoniae and Mycoplasma fermentans. The probe is flanked by anear-infrared fluorophore and a fluorescence quencher. To independentlymeasure S. aureus localization, luciferase-expressing strains of S.aureus will be used in combination with bioluminescence imaging.Co-localization of fluorescence (activated nuclease probe) withluminescence (luciferase) will indicate that the nuclease-detectingapproach can serve to detect and localize focal S. aureus infections inmice. Focal infections in mice will be induced by intramuscular (legmuscle) injection of S. aureus. Imaging and intravenous probeadministration will take place 24-48 hours after the bacterialinjection.

The oligonucleotide probe is synthesized by Integrated DNA Technologies(IDT; Coralville, Iowa). The probe consists of an 11 nucleotide-long RNAoligo (5′-CUCGUACGUUC-3′) flanked by Cy5.5 (5′-end) and a pair offluorescence quenchers, “ZEN” and “Iowa Black” (3′-end). Mice areinjected (intramuscular, leg muscle) with 100 ul (˜4×10⁶ CFU/injection)methicillin-sensitive S. aureus (MSSA) modified with the Lux operon (forLuciferase expression). 24-48 hours after administration of the S.aureus, mice are anesthetized with isofluorane and imaged (XenogenIVIS-200 System) with bioluminescence to assess the degree of infectionand with fluorescence (Cy5.5 infrared channel) to establish baselinefluorescence measurements. Then 5-10 nanomoles of the nuclease probe areinjected via tail vein and bioluminescence and fluorescence images areacquired every 5-10 minutes for 1-2 hours.

Fluorescence levels above those measured prior to probe administrationindicate the presence of activated probe. The contribution ofsubstantial fluorescence from the unactivated probe is not expected asnegligible fluorescence of the undigested probe was observed inpreliminary studies. The probe is also administered to uninfected miceto determine the dependence of probe activation on the presence of S.aureus. To determine the dynamic biodistribution of the probe, controlexperiments are carried out in which a probe missing the quenchers areadministered to infected animals and imaged at various time-points. Thecomplete probe is administered to animals infected with MN-negative S.aureus to determine the dependence of S. aureus detection on thepresence of this nuclease.

Example 5 Nuclease-Activated Probes for Imaging Staphylococcus aureusInfections

The inventors surprisingly discovered that “2′-OMe dTT” probe was moresensitive to MN (micrococcal nuclease of S. aureus) than the otherprobes, but was still resistant to degradation in serum. The inventorstested its stability in the supernatants of cultures of other pathogenicbacteria that cause similar problems as S. aureus and found that it wasnot digested by these other species. The 2′-OMe dTT probe thus isspecific for S. aureus.

Digestion of Oligonucleotide Substrates with Various Concentrations ofMicrococcal Nuclease (MN).

The degradation profile of 6 oligonucleotide substrates was evaluatedusing 4 different concentrations of MN (1 U, 0.1 U, 0.05 U and 0.01U/μl) (FIG. 5). All the sequences are flanked by a FAM at 5′- and a pairof fluorescence quenchers, “ZEN” and “Iowa Black” at the 3′-end. Thesamples were prepared as follow: PBS, 9 μl of PBS+1 μl of substrate (50pmoles); Reactions with MN include 8 μl of PBS, 1 μl of substrate(containing 50 pmoles) and 1 μl of appropriately diluted MN. All thesamples were incubated at 37° C. for 15 minutes. After the incubationperiod, 290 μl of PBS supplemented with 10 mM EDTA and 10 mM EGTA wasadded to each sample and 95 μl of each was then loaded in triplicateinto a 96-well plate (96F non-treated black microwell plate (NUNC)).Fluorescence intensity was measured with a fluorescence microplatereader (Analyst HT; Biosystems).

The oligonucleotide molecules are provided in Table 3 below.

TABLE 3 Name Length Sequence SEQ ID NO DNA 10/56-FAM/TTCCTTCCTC/ZEN//3IAbRQSp/ SEQ ID NO: 1 2′-OMe All 12 /56-SEQ ID NO: 2 FAM/mUmCmUmCmGmUmAmCmGmUmUmC/ZEN//3IAbRQSp/ 2′-F Pyr 12/56-FAM/fUfCfUfCrGfUrAfCrGfUfUfC/ZEN//3IAbRQSp/ SEQ ID NO: 3 2′-OMe dAA11 /56-FAM/mCmUmCmGAAmCmGmUmUmC/ZEN//3IAbRQSp/ SEQ ID NO: 4 2′-OMe dTT11 /56-FAM/mCmUmCmGTTmCmGmUmUmC/ZEN//3IAbRQSp/ SEQ ID NO: 5 2′-OMe dAT11 /56-FAM/mCmUmCmGATrnCmGmUmUmC/ZEN//3IAbRQSp/ SEQ ID NO: 6 /56-FAM/FAM fluorophore (fluorescein amidite) /ZEN/ ″ZEN″ fluorescence quencher/3IAbRQSp/ ″Iowa Black″ fluorescence quencher mA 2′-O-methyl modified AmC 2′-O-methyl modified C mG 2′-O-methyl modified G mU 2′-O-methylmodified U fA 2′-fluoro modified A fC 2′-fluoro modified C fG 2′-fluoromodified G fU 2′-fluoro modified U Nucleotides written in bold are deoxynucleotides (DNA)

Oligonucleotide Substrate Plate-Reader Assays:

The oligonucleotide substrates were synthesized by Integrated DNATechnologies (IDT; Coralville, Iowa). These probes consist of a 10 (DNA)or 11 nucleotide long (2′-OMe-dAA, 2′-OMe-dTT and 2′-OMe-dAT)oligonucleotide, with the chemical modifications and sequences indicatedin Table 1 above. All the sequences are flanked by a FAM at 5′-end and apair of fluorescence quenchers, “ZEN” and “Iowa Black” at the 3′-end.Five samples were assayed for degradation (FIG. 6). PBS: 1 μl of eachsubstrate (50 picomoles) was combined with 9 μl of PBS (background).Reactions with micrococcal nuclease (MN) served as positive control asthe investigators have established that the condition used here yieldsmaximal activation of the probes. These reactions include 1 μl of eachsubstrate (50 picomoles), 8 μl of PBS and 1 μl of MN (10 U/μl).Reactions with S. aureus supernatant include 1 μl of each substrate (50picomoles) and 9 μl of supernatant of a 24-hour culture of S. aureus.Reactions with mouse and human serum include 1 μl of each substrate (50picomoles) combined with 9 μl of mouse or human serum, respectively. Allthe samples were incubated at 37° C. for 1 hour. After the incubationperiod, 290 μl of PBS supplemented with 10 mM EDTA and 10 mM EGTA wasadded to each sample and 95 μl of each was then loaded in triplicateinto a 96-well plate (96F non-treated black microwell plate (NUNC)).Fluorescence intensity was measured with a fluorescence microplatereader (Analyst HT; Biosystems).

Additional data shows that the “2′-OMe dTT” probe was more sensitive toMN (micrococcal nuclease of S. aureus) than other probes, but it wasstill resistant to degradation in serum (FIGS. 5 & 6). Its stability wasthen tested in the supernatants of cultures of other pathogenic bacteriathat cause similar problems as S. aureus and it was found that it wasnot digested by these other species (FIG. 7). The 2′-OMe dTT probe thusis specific for S. aureus.

Example 6 Non-Invasive Imaging of Staphylococcus aureus Infections witha Nuclease-Activated Probe

Diagnosis of focal bacterial infections, such as osteomyelitis, septicjoints and pyomyositis initially entails the evaluation of severalnon-specific symptoms, including pain, swelling and fever. Definitiveevidence of infection and identification of the causative bacterialspecies is only possible with tissue biopsy and culture. While manyfocal bacterial infections are life-threatening situations in which timeis of-the-essence, such diagnostic procedures typically consume manyhours to days. Moreover, current diagnostic approaches, including x-rayimaging and biopsy/culture, are prone to false-negatives due to theirlow sensitivity and susceptibility to missing the infected tissue,respectively.

It has been previously reported that some bacterial nucleases canefficiently digest chemically modified oligonucleotides that areresistant to degradation by mammalian nucleases. Here, it was sought touse this observation to develop a non-invasive molecular imagingapproach for S. aureus, the most common culprit of many types of focalinfections in people. S aureus secretes a nuclease known as micrococcalnuclease (MN). A very well-studied enzyme, MN is among the firstproteins extensively investigated with structure and folding studies. MNexhibits robust DNase and RNase activities, is active on both single-and double-stranded substrates, and its nuclease activity has been usedto classify laboratory bacterial preparations for decades.

A short oligonucleotide substrate that is both sensitive to MN andresistant to serum nucleases was sought. Such an oligonucleotide couldform the basis of a quenched fluorescent imaging probe that isspecifically activated (fluorescence is unquenched) upon digestion byMN. Because the susceptibility of chemically modified oligonucleotidesubstrates to MN digestion is poorly understood, the ability of MN todegrade oligonucleotide substrates was tested with a variety of chemicalmodifications that are known to promote resistance to degradation bymammalian serum nucleases. To facilitate the subsequent development ofimaging probes, the various oligo compositions were tested in a quenchedfluorescent probe format: short (10-12mers) oligos flanked with a5′-fluorophore (FAM) and 3′-quenchers (Zen and Iowa Black RQ).

One such probe, made with an oligo composed exclusively of lockednucleic acid-modified nucleotides, was not digested by MN (FJH,unpublished observations), while oligos composed exclusively of2′-fluoro- or 2∝-O-methyl-modified nucleotides were relatively weaksubstrates. Next, the MN- and serum nuclease-susceptibility of RNAoligos composed of 2′-fluoro- or 2∝-O-methyl-modified pyrimidines andunmodified purines with a DNA oligo were compared, as DNA is thepreferred substrate for MN among unmodified nucleic acids (see Table 4for probe sequences and modifications). Concentrated MN (1 U/μl) yieldedcomplete or near-complete digestion of these oligos after shortincubations and was thus used as a normalization control for the assays.More dilute MN (0.1 U/μl) provided an intermediate degree of digestionafter 15 or 60 minutes, thus enabling assessment of the relative degreeof digestion of the substrates. As shown in FIG. 8A, the DNA probe wasdigested by MN more efficiently than either the 2′-fluoro- or2∝-O-methyl-modified pyrimidine RNA oligos, but was, as expected, alsosubstantially digested in serum. In contrast, the 2′-fluoro- and2∝-O-methyl-modified pyrimidine RNA oligos were more stable in serum,but less efficiently digested by MN. A second generation probe, composedof a pair of deoxythymidines flanked by several 2′-O-methyl modifiednucleotides, was designed to maximize sensitivity to MN, which is knownto efficiently digest poly-deoxythymidine oligos, while also resistingdegradation by serum nucleases. This “TT probe” was substantially moresensitive to MN digestion than the other chemically modified oligostested, and also exhibited robust serum stability (FIG. 8A).

To evaluate the activation of these probes in an environment that moreclosely models the physiological environment of S. aureus infections,the probes were incubated with culture supernatants of the Newman andUAMS-1 strains of S. aureus (FIG. 8B). The TT probe was completelydigested after a 60-minute incubation in either supernatant (FIG. 8B).The digestion observed here was primarily mediated by MN as incubationof the TT probe in supernatants of MN-negative versions of each strainyielded minimal probe activation (FIG. 8B). In summary, among theserum-nuclease-resistant oligos tested, the TT probe clearly exhibitedthe greatest sensitivity to digestion by MN, both in purified form andin culture supernatants.

The utility of visible light fluorophores, such as fluorescein, for invivo imaging is severely limited by tissue autofluorescence andscattering of visible light. In contrast, tissue penetration ofnear-infrared (NIR) light is much greater and tissue autofluorescencemuch reduced. Indeed, fluorescence imaging with NIR light is estimatedto be feasible at tissue depths of 7-14 centimeters. To prepare anMN-detecting imaging probe based on the TT probe that would becompatible with NIR imaging, Cy5.5, an NIR fluorophore was substitutedfor the FAM moiety used in the initial TT probe version. Thefluorescence of this intact probe was weak, but after digestion with MN,its fluorescence was comparable to that of a control probe, synthesizedwithout fluorescence quenchers.

Next, it was sought to determine whether this probe could enable thedetection of a focal S. aureus infection in mice. To provide anindependent measure of the location and amount of bacteria in infectedanimals, the lux operon was first incorporated into the Newman strain ofS. aureus and into an MN-negative modified Newman strain. Mice withunilateral thigh muscle infections (pyomyositis) of these modifiedbacteria exhibited luminescence that co-localized with gross swellingand, in some animals, externally visible lesions (FIG. 9C, 9D). Tailvein administration of 3 nanomoles (˜1 mg/kg) of Cy5.5-labeled TT probeyielded NIR fluorescence adjacent to the infection site that increasedin intensity between 15 and 45 minutes after injection (FIG. 9C). Incontrast, injection of the Cy5.5-labeled TT probe into uninfected mice(FIG. 9A) did not yield probe activation in the corresponding regions ofthese mice. Administration of the unquenched TT probe into uninfectedanimals resulted in a globally high NIR fluorescence that only began todecline 1-2 hours after injection (FIG. 9B). Finally, the probeactivation seen in the S. aureus-infected animals that received the TTprobe was primarily due to the activity of MN as substantially less TTprobe activation was seen adjacent to MN-negative S. aureus infections(FIG. 9D). This weak TT probe activation likely results from a distinctS. aureus nuclease, TT probe activation has been observed uponincubation with MN-negative S. aureus cell suspensions (data not shown).

While these results indicate that the TT probe is specifically activatedadjacent to S. aureus infection sites by MN in vivo, the reason for thelack of co-localization of the probe activation with the bacterialluminescence was uncertain. A simple and plausible explanation is thatthe intravenously administered probe may be excluded from the infectionsite in the setting of our pyomyositis infection model. To address thispossibility, the unquenched TT probe was injected into S.aureus-infected mice. The mice were subsequently sacrificed anddissected to provide a clearer picture of the infection sites. As shownin FIG. 9E, the unquenched probe is excluded from direct penetration ofthe infection site. Activation of the TT probe adjacent to, but notwithin, the infection site was also observed after sacrifice anddissection, as seen in FIG. 9F. Moreover, histological examination of S.aureus-infected mouse thigh muscles revealed lesions with substantialnecrosis, an observation consistent with the notion that the infectionsites may have reduced blood perfusion. These results suggest that theprobe activation seen in infected animals (FIG. 9C & 9F) may haveresulted from the probe encountering MN that had leaked out of theprimary infection site. In any case, the probe was able to detect thepresence of the bacteria, despite being excluded from the region wherethe bacteria, and presumably MN, were most concentrated.

The clinical diagnostic value of assays that non-invasively detectbacteria within infections such as pyomyositis, septic joints, etc.,will depend, in part, on their ability to simultaneously identify thetype of bacteria that is present. The investigators thus sought todetermine whether the TT probe, or any of the others we have tested,might also be activated by nucleases produced by any of a variety ofdistinct bacterial pathogens that cause some of the same types ofinfections as S. aureus. Of the culture supernatants of six suchbacterial species tested, none substantially digested the TT probe,while Staphylococcus lugdunensis and Streptococcus agalactiae (Group BStreptococcus) supernatants both digested the probes that included2′-fluoro modified nucleotides (FIG. 10A). Of the bacterial cellsuspensions of these cultures, only the Staphylococcus lugdunensis (ofthe same genus as S. aureus) produced any appreciable digestion (˜25%)of the TT probe in a one-hour incubation (FIG. 10B). Bacterial cellsuspensions of Streptococcus agalactiae and Streptococcus pneumoniaeboth digested the probes that included 2′-fluoro modified nucleotides(FIG. 10B). Together, these results demonstrate a high degree ofspecificity of the TT probe, and suggest that similar probes withspecificity for bacterial nucleases of a variety of species of bacterialpathogens may also be identified. Importantly, the oligonucleotideprobes digested by the Streptococcus agalactiae and Streptococcuspneumoniae cultures are resistant to serum nucleases; the nucleases ofthese bacteria thus satisfy a critical requirement for the approach wehave developed for S. aureus.

The present study is the first to demonstrate the non-invasive detectionof a bacterial infection in animals with an activatable imaging probe. Asimilar molecular imaging approach to that described here, in whichquenched fluorescent peptide-based probes that are activated bytumor-specific proteases, has provided a valuable imaging platform forcancer imaging. Because such activatable probes do not producefluorescence until the probe encounters its target, the result is ahighly sensitive means of target detection. Importantly, whilenear-infrared fluorescence (NIRF) imaging is currently only used in alimited capacity in the clinic (e.g., retinal angiography, cardiacfunction, hepatic output, sentinel lymph node dissection and colon polypidentification), advances in NIRF instrumentation are likely to expandits applicability in the near future. These developments include devicessuch as endoscopes with fluorescence imaging capabilities and externalNIRF scanners.

TABLE 4 Nuclease probe sequences and modifications. FAM-Pyr 2′F-ZRQFAM- fU fC fU fC rG fU rA fC rG fU fU fC -ZEN-RQ FAM-Pyr 2′OMe-ZRQFAM- mU mC mU mC rG mU rA mC rG mU mU mC -ZEN-RQ FAM-All 2′F-ZRQFAM- fU fC fU fC fG fU fA fC fG fU fU fC -ZEN-RQ FAM-All 2′OMe-ZRQFAM- mU mC mU mC mG mU mA mC mG mU mU mC -ZEN-RQ FAM-DNA-ZRQFAM-T T C C T T C C T C -ZEN-RQ FAM-2′-OMe+TT-ZRQ_FAM- mC mU mC mG T T mC mG mU mU mC -ZEN-RQ Cy5.5-2′-OMe+TT-ZRQ_Cy5.5- mC mU mC mG T T mC mG mU mU mC -ZEN-RQ Cy5.5-2′-OMe+TT-invTCy5.5- mC mU mC mG T T mC mG mU mU mC -InvdT FAM = FAM fluorophore(fluorescein amidite); ZEN = IDT “ZEN” fluorescence quencher; RQ = IDTIowa Black ® RQ fluorescence quencher; mA = 2′-O-methyl-Adenosine; mC =2′-O-methyl-Cytidine; mG = 2′-O-methyl-Guanosine; mU =2′-O-methy-Uridine; fA = 2′-fluoro-Adenosine; fC = 2′-fluoro-Cytidine;fG = 2′-fluoro-Guanosine; fU = 2′-fluoro-Uridine; Nucleotides written inbold are deoxy nucleotides (DNA); InvdT = inverted dT.

Materials and Methods

Oligonucleotide Probe Synthesis and Purification

Oligonucleotide probes were synthesized and purified at Integrated DNATechnologies (IDT), Coralville, Iowa Briefly, all the FAM-labeled probeswere synthesized using standard solid phase phosphoramidite chemistry,followed by high performance liquid chromatography (HPLC) purification.For the Cy5.5-labeled probes, the sequences were first synthesized withZEN and Iowa Black quenchers or inverted dT on the 3′-ends and amine onthe 5′-ends using the standard solid phase phosphoramidite chemistry,and purified with HPLC. These purified sequences were then set to reactwith Cy5.5 NHS ester (GE Healthcare, Piscataway, N.J.) to chemicallyconjugate the Cy5.5 label on the sequences. The Cy5.5-labeled probeswere further purified with a second HPLC purification. All probeidentities were confirmed by electron spray ionization mass spectrometer(ESI-MS) using an Oligo HTCS system (Novatia LLC, Princeton, N.J.). Themeasured molecular weights are within 1.5 Daltons of the expectedmolecular weights. The purity of the probes was assessed with HPLCanalysis and is typically greater than 90%. Quantitation of the probeswas achieved by calculating from their UV absorption data and theirnearest-neighbor-model-based extinction coefficients at 260 nm.Extinction coefficients of 2′-O-methyl-nucleotides and2′-fluoro-nucleotides are assumed to be the same as that of RNA.

Fluorescence Plate-Reader Nuclease Assays

Fluorescence plate reader assays were carried out as described(Hernandez et al., 2012). Briefly, for each reaction, 1 μl of a stocksolution of each probe (50 μM concentration) was combined with 9 μl ofeach sample (buffer, buffer plus recombinant nuclease, serum, culturesupernatant, culture broth or washed bacteria) and incubated at 37° C.for the time periods indicated in the figures. 290 μl of PBSsupplemented with 10 mM EDTA and 10 mM EGTA was then added to each and95 μl of each diluted reaction was loaded per well into a 96-well plate(96F non-treated black microwell plate (NUNC)). Fluorescence levels weremeasured with an Analyst HT fluorescence plate reader (LJL Biosystems).

Background fluorescence levels of probes incubated in buffer or broth,and autofluorescence levels of the various preparations were determinedand subtracted from the probe-activation reaction values as described inthe figure legends. Purified micrococcal nuclease was obtained fromWorthington Biochemical Corporation (Lakewood, N.J.). Dulbecco'sphosphate-buffered saline (DPBS) containing physiological levels ofcalcium and magnesium, was obtained from Invitrogen (Carlsbad, Calif.).Human serum was obtained from Sigma-Aldrich (St. Louis, Mo.) and mouseserum (C57BL6) was obtained from Valley Biomedical Inc. (Winchester,Va.).

Bacterial Cultures and Growth Conditions

Bacteria were maintained in tryptic soy broth (TSB), Luria Bertani (LB)or Todd Hewitt+yeast (THY) broth as defined in Table 4 for each strain.To prepare cultures for assays, overnight cultures were sub-cultured1:500 into 5 ml fresh broth and grown for 24 hr at 37° C. with shakingat 200 rpm. The only exceptions were Streptococcus pneumoniae andStreptococcus agalactiae (Group B Streptococcus), which were grown understatic conditions in a 37° C. incubator supplemented with 5.0% CO₂. Toprepare spent media for nuclease assays, 1 ml of each culture wascentrifuged at 6,000×g for 10 min and the supernatant was saved. Forpreparation of bacteria suspensions for nuclease assays, pelletedbacteria were washed with 1 ml DPBS and re-suspended in 100 μl of DPBS.

Genetic Manipulation of S. aureus

Bacteriophage 11 was used to transduce the P. luminescens luxABCDE genesfrom AH1362 into strains Newman and Newman nuc::LtrB as previouslydescribed (Novick, R. P. (1991) Genetic systems in staphylococci.Methods Enzymol 204, 587-636.). Transductants carrying the lux geneswere selected on tryptic soy agar (TSA) with kanamycin (Kan)supplemented at 50 μg/ml. The resulting strains were confirmed forbioluminescence production (lux+) using a Tecan Infinity 200M plate andsaved (see Table 5).

TABLE 5 Bacterial strains Common name Strain name of strain lineageGenotype Media used Reference Staphylococcus aureus AH1178 Newman Wildtype TSB (1) AH2495 Newman nuc::LtrB TSB (2) AH2600 Newman luxABCDE-KanTSB This work AH2672 Newman nuc::LtrB luxABCDE- TSB This work Kan AH759UAMS-1 Wild type TSB (3) AH893 UAMS-1 Δnuc TSB (4) AH1362 Xen29luxABCDE-Kan TSB (5) Staphylococcus lugdunensis AH2160 N920143 Wild typeTSB (6) Streptococcus pneumoniae AH1102 ATCC 6301 Wild type THY ATCCStreptococcus agalactiae AH2771 MN SI Wild type THY (7) Acinetobacterbaumannii AH2669 M2 Wild type LB (8) Pseudomonas aeruginosa AH71 PAO1Wild type LB (9) Klebsiella pneumoniae AH2687 43816 Wild type LB (10) Table 5 References (1). Baba, T., Bae, T., Schneewind, O., Takeuchi, F.,and Hiramatsu, K. (2008) Genome sequence of Staphylococcus aureus strainNewman and comparative analysis of staphylococcal genomes: polymorphismand evolution of two major pathogenicity islands, J. Bacteriol. 190,300-310. (2). Kiedrowski, M. R., Kavanaugh, J. S., Malone, C. L., Mootz,J. M., Voyich, J. M., Smeltzer, M. S., Bayles, K. W., and Horswill, A.R. (2011) Nuclease modulates biofilm formation in community-associatedmethicillin-resistant Staphylococcus aureus, PLoS ONE 6, e26714. (3).Gillaspy, A. F., Hickmon, S. G., Skinner, R. A., Thomas, J. R., Nelson,C. L., and Smeltzer, M. S. (1995) Role of the accessory gene regulator(agr) in pathogenesis of staphylococcal osteomyelitis, Infect. Immun.63, 3373-3380. (4). Beenken, K. E., Mrak, L. N., Griffin, L. M.,Zielinska, A. K., Shaw, L. N., Rice, K. C., Horswill, A. R., Bayles, K.W., and Smeltzer, M. S. (2010) Epistatic relationships between sarA andagr in Staphylococcus aureus biofilm formation, PLoS ONE 5, e10790. (5).Xiong, Y. Q., Willard, J., Kadurugamuwa, J. L., Yu, J., Francis, K. P.,and Bayer, A. S. (2005) Real-time in vivo bioluminescent imaging forevaluating the efficacy of antibiotics in a rat Staphylococcus aureusendocarditis model, Antimicrob. Agents Chemother. 49, 380-387. (6).Heilbronner, S., Holden, M. T., van Tonder, A., Geoghegan, J. A.,Foster, T. J., Parkhill, J., and Bentley, S. D. (2011) Genome sequenceof Staphylococcus lugdunensis N920143 allows identification of putativecolonization and virulence factors, FEMS Microbiol Lett 322, 60-67. (7).Schlievert, P. M., Varner, M., and Galask, R. P. (1983) Endotoxinenhancement as a possible cause of group B streptococcal neonatalsepsis, Obstet. Gynecol. 61, 588-592. (8). Niu, C., Clemmer, K. M.,Bonomo, R. A., and Rather, P. N. (2008) Isolation and characterizationof an autoinducer synthase from Acinetobacter baumannii, J Bacteriol190, 3386-3392. (9). Stover, C. K., Pham, X. Q., Erwin, A. L.,Mizoguchi, S. D., Warrener, P., Hickey, M. J., Brinkman, F. S.,Hufnagle, W. O., Kowalik, D. J., Lagrou, M., Garber, R. L., Goltry, L.,Tolentino, E., Westbrock-Wadman, S., Yuan, Y., Brody, L. L., Coulter, S.N., Folger, K. R., Kas, A., Larbig, K., Lim, R., Smith, K., Spencer, D.,Wong, G. K., Wu, Z., Paulsen, I. T., Reizer, J., Saier, M. H., Hancock,R. E., Lory, S., and Olson, M. V. (2000) Complete genome sequence ofPseudomonas aeruginosa PAO1, an opportunistic pathogen, Nature 406,959-964. (10). Lau, H. Y., Clegg, S., and Moore, T. A. (2007)Identification of Klebsiella pneumoniae genes uniquely expressed in astrain virulent using a murine model of bacterial pneumonia, MicrobPathog 42, 148-155.Infection of Mice with S. aureus

S. aureus cultures were prepared for injection into mice as follows. 5ml of TSB supplemented with Kan (50 μg/ml) were inoculated with frozenstocks of MN-expressing or MN-negative lux+S. aureus of the strainNewman genetic background (Table 4). Cultures were grown overnight at37° C. with shaking at 200 rpm, and each strain was sub-cultured 1:100into 5 ml of fresh media and grown for another 12 hr at 37° C. withshaking. Bacteria were washed once with PBS and resuspended in PBS to anapproximate cell density of ˜2×10⁸ CFU/ml for injection into mice.Bacteria were serially diluted, plated on TSA, and incubated at 37° C.to determine bacterial concentration.

For animal infections, 50 μl of 2×10⁸ CFU/ml (1×10⁷ CFU total) wasinjected intramuscularly (thigh muscle) in 6-8 week old C57BL6 femalemice under isoflurane anesthesia. Mice were shaved prior to injections.Injection sites were evaluated with bioluminescence imaging immediatelythereafter. Mice were imaged or sacrificed for imaging or histology 48hours after injections.

In Vivo Evaluation of Nuclease-Activated Probes

Luminescence and epifluorescence imaging was performed with a XenogenIVIS 200 imaging system (Caliper). Mice were anesthetized with 2%isoflurane gas anesthesia and placed on the imaging platform inside theoptical system for dorsal imaging. Luminescence images were recordedwith a 1 minute exposure time and an open emission filter.Epifluorescence images were acquired with a 1 second exposure time andexcitation and emission filters appropriate for the Cy5.5 dye. To avoidsaturation, the exposure time for the acquisition of epifluorescenceimages of the mice injected with the unquenched TT probe was reduced to0.5 seconds. Bioluminescence images were acquired prior to probeinjections. Fluorescence images were acquired prior to and followingtail-vein injections (time points are indicated in figures) of theprobes. For probe administration, 3 nanomoles of each probe diluted inPBS were injected via tail vein in a total volume of 120 μl. IVIS 4.2software was used to perform acquisition, imaging analysis andpreparation of pseudocolored overlays of luminescence, fluorescence andgrayscale images. Imaging of mice following sacrifice and dissection wascarried out as described for the live animal imaging, but with field ofview adjusted for image acquisitions.

Histological Analysis of Infected and Uninfected Muscle Tissue

Mice were euthanized via carbon dioxide intoxication and gross lesionswere photographed with a digital camera before and after removal of theskin. Soft tissues of the S. aureus-infected (right), and thecorresponding portion of the uninfected (left) leg were carefullydissected and fixed in 10% neutral buffered formalin for 48 hours atroom temperature. The fixed tissues were gross-sectioned and thenroutinely processed in a series of alcohol and xylene baths,paraffin-embedded, and 4 μm sections were stained with hematoxylin andeosin (HE), or Gram stain as previously described (Stoltz, D A, et al.Cystic Fibrosis Pigs Develop Lung Disease and Exhibit DefectiveBacterial Eradication at Birth. Science Translational Medicine, April28; 2(29):29ra31, 2010). Slides were examined by a veterinarypathologist (DKM) for histopathologic interpretation. High resolutiondigital images were acquired with a DP71 camera (Olympus) mounted on aBX51 microscope (Olympus) with MicroSuite Pathology Edition Software(Olympus).

Although the foregoing specification and examples fully disclose andenable the present invention, they are not intended to limit the scopeof the invention, which is defined by the claims appended hereto.

All publications, patents and patent applications are incorporatedherein by reference. While in the foregoing specification this inventionhas been described in relation to certain embodiments thereof, and manydetails have been set forth for purposes of illustration, it will beapparent to those skilled in the art that the invention is susceptibleto additional embodiments and that certain of the details describedherein may be varied considerably without departing from the basicprinciples of the invention.

The use of the terms “a” and “an” and “the” and similar referents in thecontext of describing the invention are to be construed to cover boththe singular and the plural, unless otherwise indicated herein orclearly contradicted by context. The terms “comprising,” “having,”“including,” and “containing” are to be construed as open-ended terms(i.e., meaning “including, but not limited to”) unless otherwise noted.Recitation of ranges of values herein are merely intended to serve as ashorthand method of referring individually to each separate valuefalling within the range, unless otherwise indicated herein, and eachseparate value is incorporated into the specification as if it wereindividually recited herein. All methods described herein can beperformed in any suitable order unless otherwise indicated herein orotherwise clearly contradicted by context. The use of any and allexamples, or exemplary language (e.g., “such as”) provided herein, isintended merely to better illuminate the invention and does not pose alimitation on the scope of the invention unless otherwise claimed. Nolanguage in the specification should be construed as indicating anynon-claimed element as essential to the practice of the invention.

Embodiments of this invention are described herein, including the bestmode known to the inventors for carrying out the invention. Variationsof those embodiments may become apparent to those of ordinary skill inthe art upon reading the foregoing description. The inventors expectskilled artisans to employ such variations as appropriate, and theinventors intend for the invention to be practiced otherwise than asspecifically described herein. Accordingly, this invention includes allmodifications and equivalents of the subject matter recited in theclaims appended hereto as permitted by applicable law. Moreover, anycombination of the above-described elements in all possible variationsthereof is encompassed by the invention unless otherwise indicatedherein or otherwise clearly contradicted by context.

1. A probe for detecting a microbial endonuclease comprising anoligonucleotide of 2-30 nucleotides in length, a fluorophore operablylinked to the oligonucleotide, and a quencher operably linked to theoligonucleotide, wherein the oligonucleotide comprises a modifiedpyrimidine and is capable of being cleaved by a microbial nuclease butnot by a mammalian nuclease.
 2. The probe of claim 1, wherein theoligonucleotide is 10-15 nucleotides in length.
 3. (canceled)
 4. Theprobe of claim 1, wherein the oligonucleotide has between 0-50% purines.5. The probe of claim 1, wherein one or more of the pyrimidines arechemically modified.
 6. (canceled)
 7. (canceled)
 8. The probe of claim1, wherein one or more of the purines if present are chemicallymodified.
 9. (canceled)
 10. (canceled)
 11. The probe of claim 1, whereinthe fluorophore is selected from the group consisting of thefluorophores listed in Table
 1. 12. (canceled)
 13. The probe of claim 1,wherein the quencher is selected from the group consisting of thequenchers listed in Table
 2. 14. The probe of claim 1, wherein theoligonucleotide is single-stranded.
 15. The probe of claim 1, whereinthe oligonucleotide comprises both RNA and DNA.
 16. (canceled)
 17. Theprobe of claim 15, wherein the oligonucleotide comprises a DNAdi-nucleotide.
 18. (canceled)
 19. An oligonucleotide substratecomprising a fluorophore operably linked to a first strand of 4-5modified RNA nucleotides, which is operably linked to a DNAdi-nucleotide, which is operably linked to a second strand of 4-6modified RNA nucleotides, which is operably linked to at least onefluorescence quencher.
 20. (canceled)
 21. (canceled)
 22. (canceled) 23.(canceled)
 24. (canceled)
 25. The oligonucleotide substrate of claim 19,consisting of /56-FAM/mCmUmCmGTTmCmGmUmUmC/ZEN//3IAbRQSp/ (SEQ ID NO:5).
 26. A method of detecting a microbial infection of a samplecomprising measuring fluorescence of a sample that has been contactedwith a probe of claim 1, wherein a fluorescence level that is greaterthan the fluorescence level of an uninfected control indicates that thesample has a microbial infection.
 27. The method of claim 26, whereinthe method is performed in vivo for the detection of a microbialinfection in a mammal, wherein a test fluorescence that is greater thanthe fluorescence level of an uninfected control indicates that thesample has a microbial infection.
 28. The method of claim 26, whereinthe test fluorescence level is at least 1-100% greater than the controllevel.
 29. (canceled)
 30. The method of claim 26, wherein thefluorophore is detectable at a depth of 7-14 cm in the mammal. 31.(canceled)
 32. (canceled)
 33. (canceled)
 34. (canceled)
 35. (canceled)36. (canceled)
 37. A method for detecting ribonuclease activity in atest sample, comprising: (a) contacting the test sample with asubstrate, thereby creating a test reaction mixture, wherein thesubstrate comprises a nucleic acid molecule comprising: i. a cleavagedomain comprising a single-stranded region of RNA, the single-strandedregion comprising a modified pyrimidine and; ii. a fluorescence reportergroup on one side of the internucleotide linkages; and iii. anon-fluorescent fluorescence-quenching group on the other side of theinternucleotide linkages; (b) incubating the test reaction mixture for atime sufficient for cleavage of the substrate by a ribonuclease in thesample; and (c) determining whether a detectable fluorescence signal isemitted from the test reaction mixture, wherein emission of afluorescence signal from the reaction mixture indicates that the samplecontains ribonuclease activity.
 38. The method of claim 37, furthercomprising: (d) contacting a control sample with the substrate, thecontrol sample comprising a predetermined amount of ribonuclease,thereby creating a control reaction mixture; (e) incubating the controlreaction mixture for a time sufficient for cleavage of the substrate bya ribonuclease in the control sample; and (f) determining whether adetectable fluorescence signal is emitted from the control reactionmixture; wherein detection of a greater fluorescence signal in the testreaction mixture than in the control reaction mixture indicates that thetest sample contains greater ribonuclease activity than in the controlsample, and wherein detection of a lesser fluorescence signal in thetest reaction mixture than in the control reaction mixture indicatesthat the test sample contains less ribonuclease activity than in thecontrol sample.
 39. The method of claim 38, wherein the predeterminedamount of ribonuclease is no ribonuclease, such that detection of agreater fluorescence signal in the test reaction mixture than in thecontrol reaction mixture indicates that the test sample containsribonuclease activity.
 40. The method of claim 37, further comprisingcontacting the test sample with a buffer before or during step (a). 41.A method for detecting deoxyribonuclease activity in a test sample,comprising: (a) contacting the test sample with a substrate, therebycreating a test reaction mixture, wherein the substrate comprises anucleic acid molecule comprising: i. a cleavage domain comprising asingle-stranded region of DNA, and; ii. a fluorescence reporter group onone side of the internucleotide linkages; and iii. a non-fluorescentfluorescence-quenching group on the other side of the internucleotidelinkages; (b) incubating the test reaction mixture for a time sufficientfor cleavage of the substrate by a deoxyribonuclease in the sample; and(c) determining whether a detectable fluorescence signal is emitted fromthe test reaction mixture, wherein emission of a fluorescence signalfrom the reaction mixture indicates that the sample containsdeoxyribonuclease activity.
 42. The method of claim 41, furthercomprising: (d) contacting a control sample with the substrate, thecontrol sample comprising a predetermined amount of deoxyribonuclease,thereby creating a control reaction mixture; (e) incubating the controlreaction mixture for a time sufficient for cleavage of the substrate bya deoxyribonuclease in the control sample; and (f) determining whether adetectable fluorescence signal is emitted from the control reactionmixture; wherein detection of a greater fluorescence signal in the testreaction mixture than in the control reaction mixture indicates that thetest sample contains greater deoxyribonuclease activity than in thecontrol sample, and wherein detection of a lesser fluorescence signal inthe test reaction mixture than in the control reaction mixture indicatesthat the test sample contains less deoxyribonuclease activity than inthe control sample.
 43. The method of claim 42, wherein thepredetermined amount of deoxyribonuclease is no deoxyribonuclease, suchthat detection of a greater fluorescence signal in the test reactionmixture than in the control reaction mixture indicates that the testsample contains deoxyribonuclease activity.
 44. The method of claim 41,further comprising contacting the test sample with a buffer before orduring step (a).